rs7649494

Variant names:

• chr3-152893676-A-G
• rs7649494
• ENST00000806985.1:n.174+23136A>G

Variant summary

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

The ENST00000806985.1(ENSG00000304892):​n.174+23136A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.322 in 148,618 control chromosomes in the GnomAD database, including 8,888 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 0.32 (8888 hom., cov: 23)
• Consequence: ENSG00000304892 ENST00000806985.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.12
• Publications: 3 publications found

Genes affected

ENSG00000304892 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.419 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000806985.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000304892	ENST00000806985.1		n.174+23136A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.322 AC: 47852 AN: 148502 Hom.: 8880 Cov.: 23

Gnomad AFR AF: 0.160

Gnomad AMI AF: 0.386

Gnomad AMR AF: 0.336

Gnomad ASJ AF: 0.401

Gnomad EAS AF: 0.157

Gnomad SAS AF: 0.262

Gnomad FIN AF: 0.352

Gnomad MID AF: 0.319

Gnomad NFE AF: 0.424

Gnomad OTH AF: 0.329

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

GnomAD4 genome AF: 0.322 AC: 47876 AN: 148618 Hom.: 8888 Cov.: 23 AF XY: 0.318 AC XY: 22992 AN XY: 72202

African (AFR) AF: 0.159 AC: 6454 AN: 40512

American (AMR) AF: 0.336 AC: 4972 AN: 14792

Ashkenazi Jewish (ASJ) AF: 0.401 AC: 1373 AN: 3426

East Asian (EAS) AF: 0.157 AC: 760 AN: 4844

South Asian (SAS) AF: 0.264 AC: 1208 AN: 4574

European-Finnish (FIN) AF: 0.352 AC: 3569 AN: 10144

Middle Eastern (MID) AF: 0.316 AC: 89 AN: 282

European-Non Finnish (NFE) AF: 0.424 AC: 28420 AN: 67090

Other (OTH) AF: 0.333 AC: 685 AN: 2058

Alfa AF: 0.392 Hom.: 38704

Bravo AF: 0.316

Asia WGS AF: 0.226 AC: 789 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	5.4
DANN	Benign	0.82
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs7649494; hg19: chr3-152611465;