rs7566637

Variant names:

• chr2-10282813-C-T
• rs7566637
• ENST00000757580.1:n.404+2644C>T

Variant summary

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

The ENST00000757580.1(ENSG00000298720):​n.404+2644C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.213 in 152,198 control chromosomes in the GnomAD database, including 4,032 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 0.21 (4032 hom., cov: 33)
• Consequence: ENSG00000298720 ENST00000757580.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.31
• Publications: 4 publications found

Genes affected

ENSG00000298720 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.317 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000757580.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000298720	ENST00000757580.1		n.404+2644C>T		intron	N/A
	ENSG00000298720	ENST00000757581.1		n.361-477C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.213 AC: 32399 AN: 152080 Hom.: 4010 Cov.: 33

Gnomad AFR AF: 0.321

Gnomad AMI AF: 0.252

Gnomad AMR AF: 0.162

Gnomad ASJ AF: 0.192

Gnomad EAS AF: 0.0833

Gnomad SAS AF: 0.0879

Gnomad FIN AF: 0.234

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.176

Gnomad OTH AF: 0.193

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

GnomAD4 genome AF: 0.213 AC: 32461 AN: 152198 Hom.: 4032 Cov.: 33 AF XY: 0.214 AC XY: 15922 AN XY: 74422

African (AFR) AF: 0.322 AC: 13358 AN: 41488

American (AMR) AF: 0.162 AC: 2481 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.192 AC: 664 AN: 3466

East Asian (EAS) AF: 0.0837 AC: 434 AN: 5186

South Asian (SAS) AF: 0.0888 AC: 429 AN: 4830

European-Finnish (FIN) AF: 0.234 AC: 2480 AN: 10604

Middle Eastern (MID) AF: 0.143 AC: 42 AN: 294

European-Non Finnish (NFE) AF: 0.176 AC: 11939 AN: 68008

Other (OTH) AF: 0.191 AC: 404 AN: 2112

Alfa AF: 0.189 Hom.: 2112

Bravo AF: 0.212

Asia WGS AF: 0.0970 AC: 338 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.053
DANN	Benign	0.33
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs7566637; hg19: chr2-10422939;