rs2894891

Variant names:

• chr6-99762031-T-C
• rs2894891

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 0.33 in 152,124 control chromosomes in the GnomAD database, including 9,949 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 0.33 (9949 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0630

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.421 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: 0.330 AC: 50226 AN: 152006 Hom.: 9953 Cov.: 32

Gnomad AFR AF: 0.112

Gnomad AMI AF: 0.291

Gnomad AMR AF: 0.398

Gnomad ASJ AF: 0.476

Gnomad EAS AF: 0.341

Gnomad SAS AF: 0.333

Gnomad FIN AF: 0.412

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.425

Gnomad OTH AF: 0.377

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

GnomAD4 genome AF: 0.330 AC: 50229 AN: 152124 Hom.: 9949 Cov.: 32 AF XY: 0.330 AC XY: 24520 AN XY: 74364

Gnomad4 AFR AF: 0.112

Gnomad4 AMR AF: 0.399

Gnomad4 ASJ AF: 0.476

Gnomad4 EAS AF: 0.341

Gnomad4 SAS AF: 0.332

Gnomad4 FIN AF: 0.412

Gnomad4 NFE AF: 0.425

Gnomad4 OTH AF: 0.373

Alfa AF: 0.404 Hom.: 7010

Bravo AF: 0.323

Asia WGS AF: 0.324 AC: 1124 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	8.7
DANN	Benign	0.88

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2894891; hg19: chr6-100209907;