rs41268884

Positions:

• chr6-31585691-A-G

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;