rs7639012

Variant names:

• chr3-154497318-C-A
• rs7639012

Your query was ambiguous. Multiple possible variants found:

• chr3-154497318-C-A
• chr3-154497318-C-T

Variant summary

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

The variant allele was found at a frequency of 0.0601 in 152,276 control chromosomes in the GnomAD database, including 364 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 0.060 (364 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.455
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.62).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0767 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0601 AC: 9147 AN: 152158 Hom.: 364 Cov.: 32

Gnomad AFR AF: 0.0397

Gnomad AMI AF: 0.0395

Gnomad AMR AF: 0.0566

Gnomad ASJ AF: 0.123

Gnomad EAS AF: 0.000577

Gnomad SAS AF: 0.0592

Gnomad FIN AF: 0.0376

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0784

Gnomad OTH AF: 0.0689

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

GnomAD4 genome AF: 0.0601 AC: 9151 AN: 152276 Hom.: 364 Cov.: 32 AF XY: 0.0578 AC XY: 4306 AN XY: 74452

African (AFR) AF: 0.0396 AC: 1647 AN: 41550

American (AMR) AF: 0.0565 AC: 864 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.123 AC: 426 AN: 3470

East Asian (EAS) AF: 0.000578 AC: 3 AN: 5188

South Asian (SAS) AF: 0.0597 AC: 288 AN: 4828

European-Finnish (FIN) AF: 0.0376 AC: 399 AN: 10610

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.0784 AC: 5334 AN: 68024

Other (OTH) AF: 0.0682 AC: 144 AN: 2112

Alfa AF: 0.0327 Hom.: 19

Bravo AF: 0.0596

Asia WGS AF: 0.0210 AC: 73 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.62
CADD	Benign	15
DANN	Benign	0.84
PhyloP100		0.46

Splicing

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

Other links and lift over

dbSNP: rs7639012; hg19: chr3-154215107;