rs934774

Variant names:

• chr2-85671020-C-A
• rs934774

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 0.3 in 151,778 control chromosomes in the GnomAD database, including 8,031 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 0.30 (8031 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.55

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 (EAS) allele frequency at 95% confidence interval = 0.464 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: 0.300 AC: 45505 AN: 151658 Hom.: 8030 Cov.: 29

Gnomad AFR AF: 0.104

Gnomad AMI AF: 0.454

Gnomad AMR AF: 0.367

Gnomad ASJ AF: 0.460

Gnomad EAS AF: 0.478

Gnomad SAS AF: 0.408

Gnomad FIN AF: 0.318

Gnomad MID AF: 0.471

Gnomad NFE AF: 0.368

Gnomad OTH AF: 0.339

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

GnomAD4 genome AF: 0.300 AC: 45505 AN: 151778 Hom.: 8031 Cov.: 29 AF XY: 0.302 AC XY: 22369 AN XY: 74156

Gnomad4 AFR AF: 0.104

Gnomad4 AMR AF: 0.367

Gnomad4 ASJ AF: 0.460

Gnomad4 EAS AF: 0.480

Gnomad4 SAS AF: 0.408

Gnomad4 FIN AF: 0.318

Gnomad4 NFE AF: 0.368

Gnomad4 OTH AF: 0.341

Alfa AF: 0.368 Hom.: 19453

Bravo AF: 0.296

Asia WGS AF: 0.422 AC: 1466 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	4.9
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs934774; hg19: chr2-85898143;