10-2501636-C-T

Variant names:

• chr10-2501636-C-T
• rs912553422
• XM_011519770.3:c.312G>A

Variant summary

Our verdict is Benign. The variant received -11 ACMG points: 0P and 11B. BP4_Strong BP6_Moderate BP7 BS2

The XM_011519770.3(LOC107983989):​c.312G>A​(p.Pro104Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00317 in 148,738 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.0032 (3 hom., cov: 28)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: LOC107983989 XM_011519770.3 synonymous
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.117
• Publications: 0 publications found

Genes affected

LOC107983989 (HGNC:):

LINC02645 (HGNC:54129): (long intergenic non-protein coding RNA 2645)

ACMG classification

Our verdict: Benign. The variant received -11 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BP6: Variant 10-2501636-C-T is Benign according to our data. Variant chr10-2501636-C-T is described in ClinVar as Likely_benign. ClinVar VariationId is 3025850.Status of the report is criteria_provided_single_submitter, 1 stars.
• BP7: Synonymous conserved (PhyloP=0.117 with no splicing effect.
• BS2: High Homozygotes in GnomAd4 at 3 gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000414107.6. 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
	LINC02645	NR_136146.1		n.-174G>A		upstream_gene	N/A
	LOC105376350	NR_188171.1		n.-217C>T		upstream_gene	N/A
	LOC105376350	NR_188172.1		n.-217C>T		upstream_gene	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02645	ENST00000414107.6	TSL:3	n.80G>A		non_coding_transcript_exon	Exon 2 of 4
	ENSG00000235281	ENST00000438753.2	TSL:5	n.328C>T		non_coding_transcript_exon	Exon 1 of 2
	ENSG00000235281	ENST00000656735.1		n.11C>T		non_coding_transcript_exon	Exon 1 of 4

Frequencies

GnomAD3 genomes AF: 0.00317 AC: 471 AN: 148646 Hom.: 3 Cov.: 28

Gnomad AFR AF: 0.00127

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00254

Gnomad ASJ AF: 0.000581

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000214

Gnomad FIN AF: 0.00137

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00539

Gnomad OTH AF: 0.00244

GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0 AN: 348 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 260

African (AFR) AF: 0.00 AC: 0 AN: 8

American (AMR) AF: 0.00 AC: 0 AN: 8

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 6

East Asian (EAS) AF: 0.00 AC: 0 AN: 18

South Asian (SAS) AF: 0.00 AC: 0 AN: 10

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 54

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 222

Other (OTH) AF: 0.00 AC: 0 AN: 20

GnomAD4 genome AF: 0.00317 AC: 471 AN: 148738 Hom.: 3 Cov.: 28 AF XY: 0.00274 AC XY: 199 AN XY: 72676

African (AFR) AF: 0.00126 AC: 51 AN: 40410

American (AMR) AF: 0.00254 AC: 38 AN: 14990

Ashkenazi Jewish (ASJ) AF: 0.000581 AC: 2 AN: 3442

East Asian (EAS) AF: 0.00 AC: 0 AN: 5022

South Asian (SAS) AF: 0.000214 AC: 1 AN: 4664

European-Finnish (FIN) AF: 0.00137 AC: 14 AN: 10250

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 266

European-Non Finnish (NFE) AF: 0.00539 AC: 360 AN: 66730

Other (OTH) AF: 0.00242 AC: 5 AN: 2068

Alfa AF: 0.00489 Hom.: 0

ClinVar

ClinVar submissions

Significance: Likely benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	9.6
DANN	Benign	0.84
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs912553422; hg19: chr10-2543828;