rs954493

Variant names:

• chr3-36707686-G-A
• rs954493

Your query was ambiguous. Multiple possible variants found:

• chr3-36707686-G-A
• chr3-36707686-G-C

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 0.234 in 152,056 control chromosomes in the GnomAD database, including 4,565 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 0.23 (4565 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.370

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.323 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: 0.234 AC: 35478 AN: 151938 Hom.: 4538 Cov.: 31

Gnomad AFR AF: 0.327

Gnomad AMI AF: 0.290

Gnomad AMR AF: 0.161

Gnomad ASJ AF: 0.165

Gnomad EAS AF: 0.143

Gnomad SAS AF: 0.176

Gnomad FIN AF: 0.182

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.215

Gnomad OTH AF: 0.235

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

GnomAD4 genome AF: 0.234 AC: 35556 AN: 152056 Hom.: 4565 Cov.: 31 AF XY: 0.231 AC XY: 17193 AN XY: 74350

Gnomad4 AFR AF: 0.328

Gnomad4 AMR AF: 0.160

Gnomad4 ASJ AF: 0.165

Gnomad4 EAS AF: 0.143

Gnomad4 SAS AF: 0.178

Gnomad4 FIN AF: 0.182

Gnomad4 NFE AF: 0.215

Gnomad4 OTH AF: 0.236

Alfa AF: 0.215 Hom.: 5102

Bravo AF: 0.237

Asia WGS AF: 0.169 AC: 589 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	2.5
DANN	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs954493; hg19: chr3-36749177;