rs9267444

Variant names:

• chr6-31515681-G-A
• rs9267444

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 0.392 in 151,946 control chromosomes in the GnomAD database, including 12,044 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 0.39 (12044 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.23
• Publications: 23 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.463 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.392 AC: 59553 AN: 151830 Hom.: 12030 Cov.: 31

Gnomad AFR AF: 0.469

Gnomad AMI AF: 0.478

Gnomad AMR AF: 0.394

Gnomad ASJ AF: 0.297

Gnomad EAS AF: 0.371

Gnomad SAS AF: 0.186

Gnomad FIN AF: 0.418

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.362

Gnomad OTH AF: 0.374

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

GnomAD4 genome AF: 0.392 AC: 59602 AN: 151946 Hom.: 12044 Cov.: 31 AF XY: 0.389 AC XY: 28899 AN XY: 74258

African (AFR) AF: 0.469 AC: 19433 AN: 41438

American (AMR) AF: 0.394 AC: 6012 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.297 AC: 1031 AN: 3468

East Asian (EAS) AF: 0.372 AC: 1913 AN: 5146

South Asian (SAS) AF: 0.186 AC: 895 AN: 4818

European-Finnish (FIN) AF: 0.418 AC: 4413 AN: 10550

Middle Eastern (MID) AF: 0.289 AC: 85 AN: 294

European-Non Finnish (NFE) AF: 0.362 AC: 24606 AN: 67954

Other (OTH) AF: 0.371 AC: 780 AN: 2104

Alfa AF: 0.386 Hom.: 13712

Bravo AF: 0.396

Asia WGS AF: 0.242 AC: 843 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.3
DANN	Benign	0.43
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs9267444; hg19: chr6-31483458;