rs6901854

Variant names:

• chr6-100484415-C-T
• rs6901854

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 0.523 in 152,042 control chromosomes in the GnomAD database, including 20,971 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 0.52 (20971 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.35

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.57).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.646 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: 0.524 AC: 79538 AN: 151924 Hom.: 20955 Cov.: 32

Gnomad AFR AF: 0.500

Gnomad AMI AF: 0.429

Gnomad AMR AF: 0.474

Gnomad ASJ AF: 0.505

Gnomad EAS AF: 0.366

Gnomad SAS AF: 0.666

Gnomad FIN AF: 0.542

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.550

Gnomad OTH AF: 0.531

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

GnomAD4 genome AF: 0.523 AC: 79585 AN: 152042 Hom.: 20971 Cov.: 32 AF XY: 0.524 AC XY: 38950 AN XY: 74320

Gnomad4 AFR AF: 0.500

Gnomad4 AMR AF: 0.475

Gnomad4 ASJ AF: 0.505

Gnomad4 EAS AF: 0.366

Gnomad4 SAS AF: 0.665

Gnomad4 FIN AF: 0.542

Gnomad4 NFE AF: 0.550

Gnomad4 OTH AF: 0.526

Alfa AF: 0.551 Hom.: 12396

Bravo AF: 0.510

Asia WGS AF: 0.505 AC: 1758 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.57
CADD	Benign	19
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6901854; hg19: chr6-100932291; COSMIC: COSV60255606;