rs138183110

Variant names:

• chr11-19225332-G-A
• rs138183110
• NM_024680.4:c.2310C>T

Your query was ambiguous. Multiple possible variants found:

• chr11-19225332-G-A
• chr11-19225332-G-T

Variant summary

Our verdict is Benign. The variant received -17 ACMG points: 0P and 17B. BP4_Strong BP6_Very_Strong BP7 BS2

The NM_024680.4(E2F8):​c.2310C>T​(p.Val770Val) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000655 in 1,614,106 control chromosomes in the GnomAD database, including 8 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.0037 (4 hom., cov: 32)
  • Exomes 𝑓: 0.00034 (4 hom.)
• Consequence: E2F8 NM_024680.4 synonymous
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: 0.620
• Publications: 1 publications found

Genes affected

E2F8 (HGNC:24727): (E2F transcription factor 8) This gene encodes a member of a family of transcription factors which regulate the expression of genes required for progression through the cell cycle. The encoded protein regulates progression from G1 to S phase by ensuring the nucleus divides at the proper time. Multiple alternatively spliced variants, encoding the same protein, have been identified. [provided by RefSeq, Jan 2012]

CSRP3-AS1 (HGNC:54183): (CSRP3 and E2F8 antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -17 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BP6: Variant 11-19225332-G-A is Benign according to our data. Variant chr11-19225332-G-A is described in ClinVar as Benign. ClinVar VariationId is 709992.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BP7: Synonymous conserved (PhyloP=0.62 with no splicing effect.
• BS2: High Homozygotes in GnomAd4 at 4 gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_024680.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	E2F8	NM_024680.4	MANE Select	c.2310C>T	p.Val770Val	synonymous	Exon 12 of 13	NP_078956.2
	E2F8	NM_001256371.2		c.2310C>T	p.Val770Val	synonymous	Exon 12 of 13	NP_001243300.1	A0AVK6
	E2F8	NM_001256372.1		c.2310C>T	p.Val770Val	synonymous	Exon 12 of 13	NP_001243301.1	A0AVK6

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	E2F8	ENST00000250024.9	TSL:1 MANE Select	c.2310C>T	p.Val770Val	synonymous	Exon 12 of 13	ENSP00000250024.4	A0AVK6
	E2F8	ENST00000928104.1		c.2334C>T	p.Val778Val	synonymous	Exon 12 of 13	ENSP00000598163.1
	E2F8	ENST00000527884.5	TSL:2	c.2310C>T	p.Val770Val	synonymous	Exon 12 of 13	ENSP00000434199.1	A0AVK6

Frequencies

GnomAD3 genomes AF: 0.00366 AC: 556 AN: 152100 Hom.: 4 Cov.: 32

Gnomad AFR AF: 0.0129

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000918

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000588

Gnomad OTH AF: 0.00143

GnomAD2 exomes AF: 0.000871 AC: 219 AN: 251470 AF XY: 0.000640

Gnomad AFR exome AF: 0.0119

Gnomad AMR exome AF: 0.000549

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.0000264

Gnomad OTH exome AF: 0.000326

GnomAD4 exome AF: 0.000342 AC: 500 AN: 1461888 Hom.: 4 Cov.: 31 AF XY: 0.000282 AC XY: 205 AN XY: 727246

African (AFR) AF: 0.0122 AC: 410 AN: 33480

American (AMR) AF: 0.000648 AC: 29 AN: 44724

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 26136

East Asian (EAS) AF: 0.00 AC: 0 AN: 39700

South Asian (SAS) AF: 0.0000116 AC: 1 AN: 86258

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 53420

Middle Eastern (MID) AF: 0.000347 AC: 2 AN: 5764

European-Non Finnish (NFE) AF: 0.0000162 AC: 18 AN: 1112010

Other (OTH) AF: 0.000662 AC: 40 AN: 60396

GnomAD4 genome AF: 0.00366 AC: 557 AN: 152218 Hom.: 4 Cov.: 32 AF XY: 0.00343 AC XY: 255 AN XY: 74436

African (AFR) AF: 0.0129 AC: 536 AN: 41524

American (AMR) AF: 0.000916 AC: 14 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3472

East Asian (EAS) AF: 0.00 AC: 0 AN: 5174

South Asian (SAS) AF: 0.00 AC: 0 AN: 4828

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10598

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.0000588 AC: 4 AN: 68026

Other (OTH) AF: 0.00142 AC: 3 AN: 2114

Alfa AF: 0.00119 Hom.: 1

Bravo AF: 0.00376

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, multiple submitters, no conflicts

Pathogenic	VUS	Benign	Condition
-	-	2	not provided (2)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	3.6
DANN	Benign	0.74
PhyloP100		0.62
Mutation Taster		=100/0	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs138183110; hg19: chr11-19246879;