rs12650313

Variant names:

• chr4-41705076-G-A
• rs12650313

Your query was ambiguous. Multiple possible variants found:

• chr4-41705076-G-A
• chr4-41705076-G-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 0.155 in 152,148 control chromosomes in the GnomAD database, including 2,215 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 0.15 (2215 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.24
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.259 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: 0.154 AC: 23477 AN: 152030 Hom.: 2202 Cov.: 32

Gnomad AFR AF: 0.262

Gnomad AMI AF: 0.0482

Gnomad AMR AF: 0.171

Gnomad ASJ AF: 0.0769

Gnomad EAS AF: 0.138

Gnomad SAS AF: 0.142

Gnomad FIN AF: 0.160

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.0929

Gnomad OTH AF: 0.122

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

GnomAD4 genome AF: 0.155 AC: 23534 AN: 152148 Hom.: 2215 Cov.: 32 AF XY: 0.158 AC XY: 11785 AN XY: 74382

African (AFR) AF: 0.263 AC: 10908 AN: 41498

American (AMR) AF: 0.171 AC: 2610 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0769 AC: 267 AN: 3470

East Asian (EAS) AF: 0.138 AC: 714 AN: 5174

South Asian (SAS) AF: 0.142 AC: 686 AN: 4824

European-Finnish (FIN) AF: 0.160 AC: 1697 AN: 10596

Middle Eastern (MID) AF: 0.126 AC: 37 AN: 294

European-Non Finnish (NFE) AF: 0.0929 AC: 6317 AN: 67986

Other (OTH) AF: 0.120 AC: 254 AN: 2114

Alfa AF: 0.109 Hom.: 1860

Bravo AF: 0.159

Asia WGS AF: 0.146 AC: 508 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.47
DANN	Benign	0.58
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs12650313; hg19: chr4-41707093;