rs41268884

Variant names:

• chr6-31585691-A-G
• rs41268884

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 0.104 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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.0514

Gnomad4 AMR AF: 0.0969

Gnomad4 ASJ AF: 0.125

Gnomad4 EAS AF: 0.102

Gnomad4 SAS AF: 0.0815

Gnomad4 FIN AF: 0.137

Gnomad4 NFE AF: 0.135

Gnomad4 OTH AF: 0.116

Alfa AF: 0.119 Hom.: 293

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

Splicing

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

Publications

LitVar

Other links and lift over

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