rs267487

Positions:

• chr3-6441869-A-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 0.211 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.326

Gnomad4 AMR AF: 0.191

Gnomad4 ASJ AF: 0.177

Gnomad4 EAS AF: 0.446

Gnomad4 SAS AF: 0.312

Gnomad4 FIN AF: 0.116

Gnomad4 NFE AF: 0.139

Gnomad4 OTH AF: 0.198

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs267487; hg19: chr3-6483556;