rs41268884

Variant names:

• chr6-31585691-A-G
• rs41268884

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 0.104 in 151,542 control chromosomes in the GnomAD database, including 954 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 0.10 (954 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.316
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.132 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: 0.104 AC: 15799 AN: 151424 Hom.: 956 Cov.: 29

Gnomad AFR AF: 0.0515

Gnomad AMI AF: 0.0208

Gnomad AMR AF: 0.0967

Gnomad ASJ AF: 0.125

Gnomad EAS AF: 0.102

Gnomad SAS AF: 0.0816

Gnomad FIN AF: 0.137

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.135

Gnomad OTH AF: 0.117

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

GnomAD4 genome AF: 0.104 AC: 15802 AN: 151542 Hom.: 954 Cov.: 29 AF XY: 0.103 AC XY: 7635 AN XY: 74002

African (AFR) AF: 0.0514 AC: 2122 AN: 41308

American (AMR) AF: 0.0969 AC: 1471 AN: 15186

Ashkenazi Jewish (ASJ) AF: 0.125 AC: 433 AN: 3468

East Asian (EAS) AF: 0.102 AC: 525 AN: 5142

South Asian (SAS) AF: 0.0815 AC: 390 AN: 4788

European-Finnish (FIN) AF: 0.137 AC: 1443 AN: 10516

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.135 AC: 9127 AN: 67830

Other (OTH) AF: 0.116 AC: 244 AN: 2098

Alfa AF: 0.115 Hom.: 588

Bravo AF: 0.101

Asia WGS AF: 0.0960 AC: 334 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	3.9
DANN	Benign	0.66
PhyloP100		-0.32
PromoterAI		0.040	Neutral

Splicing

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

Other links and lift over

dbSNP: rs41268884; hg19: chr6-31553468; COSMIC: COSV53001156;