rs934774

Variant names:

• chr2-85671020-C-A
• rs934774

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 12 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.104 AC: 4312 AN: 41462

American (AMR) AF: 0.367 AC: 5592 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.460 AC: 1594 AN: 3468

East Asian (EAS) AF: 0.480 AC: 2446 AN: 5100

South Asian (SAS) AF: 0.408 AC: 1952 AN: 4786

European-Finnish (FIN) AF: 0.318 AC: 3341 AN: 10518

Middle Eastern (MID) AF: 0.473 AC: 138 AN: 292

European-Non Finnish (NFE) AF: 0.368 AC: 25000 AN: 67890

Other (OTH) AF: 0.341 AC: 717 AN: 2104

Alfa AF: 0.349 Hom.: 29110

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
PhyloP100		1.6

Splicing

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

Other links and lift over

dbSNP: rs934774; hg19: chr2-85898143;