rs2613675

Variant names:

• chr8-21193724-A-G
• rs2613675
• ENST00000657734.1:n.1326+101410T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000657734.1(ENSG00000254092):​n.1326+101410T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.444 in 152,032 control chromosomes in the GnomAD database, including 19,367 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.44 (19367 hom., cov: 32)
• Consequence: ENSG00000254092 ENST00000657734.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.40
• Publications: 2 publications found

Genes affected

ENSG00000254092 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.811 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000657734.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000254092	ENST00000657734.1		n.1326+101410T>C		intron	N/A
	ENSG00000254092	ENST00000659453.1		n.1639+101410T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.444 AC: 67411 AN: 151914 Hom.: 19317 Cov.: 32

Gnomad AFR AF: 0.818

Gnomad AMI AF: 0.231

Gnomad AMR AF: 0.349

Gnomad ASJ AF: 0.378

Gnomad EAS AF: 0.256

Gnomad SAS AF: 0.471

Gnomad FIN AF: 0.224

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.290

Gnomad OTH AF: 0.432

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.444 AC: 67511 AN: 152032 Hom.: 19367 Cov.: 32 AF XY: 0.440 AC XY: 32699 AN XY: 74336

African (AFR) AF: 0.819 AC: 33937 AN: 41460

American (AMR) AF: 0.349 AC: 5326 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.378 AC: 1310 AN: 3468

East Asian (EAS) AF: 0.256 AC: 1321 AN: 5170

South Asian (SAS) AF: 0.473 AC: 2277 AN: 4818

European-Finnish (FIN) AF: 0.224 AC: 2374 AN: 10596

Middle Eastern (MID) AF: 0.442 AC: 129 AN: 292

European-Non Finnish (NFE) AF: 0.290 AC: 19727 AN: 67944

Other (OTH) AF: 0.428 AC: 899 AN: 2100

Alfa AF: 0.351 Hom.: 35848

Bravo AF: 0.470

Asia WGS AF: 0.407 AC: 1418 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.091
DANN	Benign	0.41
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs2613675; hg19: chr8-21051235;