rs267487

Variant names:

• chr3-6441869-A-T
• rs267487

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 0.211 in 151,260 control chromosomes in the GnomAD database, including 4,078 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 0.21 (4078 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.339
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.431 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: 0.211 AC: 31875 AN: 151156 Hom.: 4068 Cov.: 30

Gnomad AFR AF: 0.326

Gnomad AMI AF: 0.0910

Gnomad AMR AF: 0.190

Gnomad ASJ AF: 0.177

Gnomad EAS AF: 0.446

Gnomad SAS AF: 0.311

Gnomad FIN AF: 0.116

Gnomad MID AF: 0.296

Gnomad NFE AF: 0.139

Gnomad OTH AF: 0.201

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

GnomAD4 genome AF: 0.211 AC: 31909 AN: 151260 Hom.: 4078 Cov.: 30 AF XY: 0.214 AC XY: 15794 AN XY: 73862

African (AFR) AF: 0.326 AC: 13418 AN: 41170

American (AMR) AF: 0.191 AC: 2893 AN: 15178

Ashkenazi Jewish (ASJ) AF: 0.177 AC: 612 AN: 3462

East Asian (EAS) AF: 0.446 AC: 2281 AN: 5112

South Asian (SAS) AF: 0.312 AC: 1495 AN: 4786

European-Finnish (FIN) AF: 0.116 AC: 1204 AN: 10364

Middle Eastern (MID) AF: 0.293 AC: 85 AN: 290

European-Non Finnish (NFE) AF: 0.139 AC: 9423 AN: 67892

Other (OTH) AF: 0.198 AC: 415 AN: 2094

Alfa AF: 0.173 Hom.: 321

Bravo AF: 0.223

Asia WGS AF: 0.357 AC: 1239 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.9
DANN	Benign	0.31
PhyloP100		0.34

Splicing

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

Other links and lift over

dbSNP: rs267487; hg19: chr3-6483556;