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. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.0396

Gnomad4 AMR AF: 0.0565

Gnomad4 ASJ AF: 0.123

Gnomad4 EAS AF: 0.000578

Gnomad4 SAS AF: 0.0597

Gnomad4 FIN AF: 0.0376

Gnomad4 NFE AF: 0.0784

Gnomad4 OTH AF: 0.0682

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7639012; hg19: chr3-154215107;