rs3954895

Variant names:

• chr8-70547011-C-G
• rs3954895

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 0.422 in 151,962 control chromosomes in the GnomAD database, including 14,459 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 0.42 (14459 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0520

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.877 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: 0.421 AC: 63960 AN: 151844 Hom.: 14423 Cov.: 31

Gnomad AFR AF: 0.430

Gnomad AMI AF: 0.282

Gnomad AMR AF: 0.480

Gnomad ASJ AF: 0.250

Gnomad EAS AF: 0.899

Gnomad SAS AF: 0.389

Gnomad FIN AF: 0.394

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.385

Gnomad OTH AF: 0.397

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

GnomAD4 genome AF: 0.422 AC: 64063 AN: 151962 Hom.: 14459 Cov.: 31 AF XY: 0.425 AC XY: 31573 AN XY: 74306

Gnomad4 AFR AF: 0.431

Gnomad4 AMR AF: 0.480

Gnomad4 ASJ AF: 0.250

Gnomad4 EAS AF: 0.899

Gnomad4 SAS AF: 0.390

Gnomad4 FIN AF: 0.394

Gnomad4 NFE AF: 0.385

Gnomad4 OTH AF: 0.402

Alfa AF: 0.398 Hom.: 1494

Bravo AF: 0.434

Asia WGS AF: 0.647 AC: 2248 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.52
DANN	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3954895; hg19: chr8-71459246;