rs300774

Variant names:

• chr2-112496-A-C
• rs300774

Your query was ambiguous. Multiple possible variants found:

• chr2-112496-A-C
• chr2-112496-A-G
• chr2-112496-A-T

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 0.81 in 152,094 control chromosomes in the GnomAD database, including 50,070 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 0.81 (50070 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.151
• Publications: 33 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.869 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: 0.810 AC: 123074 AN: 151976 Hom.: 50039 Cov.: 32

Gnomad AFR AF: 0.825

Gnomad AMI AF: 0.863

Gnomad AMR AF: 0.716

Gnomad ASJ AF: 0.814

Gnomad EAS AF: 0.891

Gnomad SAS AF: 0.680

Gnomad FIN AF: 0.872

Gnomad MID AF: 0.775

Gnomad NFE AF: 0.815

Gnomad OTH AF: 0.788

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

GnomAD4 genome AF: 0.810 AC: 123150 AN: 152094 Hom.: 50070 Cov.: 32 AF XY: 0.809 AC XY: 60141 AN XY: 74338

African (AFR) AF: 0.825 AC: 34195 AN: 41448

American (AMR) AF: 0.715 AC: 10928 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.814 AC: 2826 AN: 3470

East Asian (EAS) AF: 0.890 AC: 4611 AN: 5178

South Asian (SAS) AF: 0.681 AC: 3278 AN: 4816

European-Finnish (FIN) AF: 0.872 AC: 9230 AN: 10580

Middle Eastern (MID) AF: 0.769 AC: 226 AN: 294

European-Non Finnish (NFE) AF: 0.815 AC: 55420 AN: 68016

Other (OTH) AF: 0.783 AC: 1649 AN: 2106

Alfa AF: 0.813 Hom.: 149685

Bravo AF: 0.797

Asia WGS AF: 0.746 AC: 2597 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.86
DANN	Benign	0.40
PhyloP100		-0.15

Splicing

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

Other links and lift over

dbSNP: rs300774; hg19: chr2-112496;