rs155207

Variant names:

• chr3-6470026-C-A
• rs155207

Your query was ambiguous. Multiple possible variants found:

• chr3-6470026-C-A
• chr3-6470026-C-G

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 0.312 in 151,812 control chromosomes in the GnomAD database, including 8,905 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 0.31 (8905 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.390

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.516 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: 0.312 AC: 47357 AN: 151694 Hom.: 8871 Cov.: 31

Gnomad AFR AF: 0.522

Gnomad AMI AF: 0.135

Gnomad AMR AF: 0.320

Gnomad ASJ AF: 0.284

Gnomad EAS AF: 0.262

Gnomad SAS AF: 0.351

Gnomad FIN AF: 0.160

Gnomad MID AF: 0.283

Gnomad NFE AF: 0.212

Gnomad OTH AF: 0.311

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

GnomAD4 genome AF: 0.312 AC: 47441 AN: 151812 Hom.: 8905 Cov.: 31 AF XY: 0.312 AC XY: 23187 AN XY: 74216

Gnomad4 AFR AF: 0.522

Gnomad4 AMR AF: 0.321

Gnomad4 ASJ AF: 0.284

Gnomad4 EAS AF: 0.262

Gnomad4 SAS AF: 0.351

Gnomad4 FIN AF: 0.160

Gnomad4 NFE AF: 0.212

Gnomad4 OTH AF: 0.310

Alfa AF: 0.257 Hom.: 741

Bravo AF: 0.330

Asia WGS AF: 0.368 AC: 1278 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.34
DANN	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs155207; hg19: chr3-6511713;