rs12735613

Variant names:

• chr1-118341350-G-A
• rs12735613

Your query was ambiguous. Multiple possible variants found:

• chr1-118341350-G-A
• chr1-118341350-G-C
• chr1-118341350-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 0.223 in 151,944 control chromosomes in the GnomAD database, including 3,952 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 0.22 (3952 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0120
• Publications: 33 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.286 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: 0.224 AC: 33942 AN: 151826 Hom.: 3960 Cov.: 32

Gnomad AFR AF: 0.174

Gnomad AMI AF: 0.203

Gnomad AMR AF: 0.234

Gnomad ASJ AF: 0.298

Gnomad EAS AF: 0.285

Gnomad SAS AF: 0.299

Gnomad FIN AF: 0.236

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.236

Gnomad OTH AF: 0.213

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

GnomAD4 genome AF: 0.223 AC: 33931 AN: 151944 Hom.: 3952 Cov.: 32 AF XY: 0.224 AC XY: 16672 AN XY: 74282

African (AFR) AF: 0.174 AC: 7194 AN: 41438

American (AMR) AF: 0.233 AC: 3561 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.298 AC: 1033 AN: 3470

East Asian (EAS) AF: 0.285 AC: 1469 AN: 5156

South Asian (SAS) AF: 0.299 AC: 1439 AN: 4810

European-Finnish (FIN) AF: 0.236 AC: 2482 AN: 10538

Middle Eastern (MID) AF: 0.214 AC: 63 AN: 294

European-Non Finnish (NFE) AF: 0.236 AC: 16061 AN: 67962

Other (OTH) AF: 0.211 AC: 444 AN: 2108

Alfa AF: 0.232 Hom.: 15075

Bravo AF: 0.219

Asia WGS AF: 0.264 AC: 917 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.8
DANN	Benign	0.40
PhyloP100		0.012

Splicing

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

Other links and lift over

dbSNP: rs12735613; hg19: chr1-118883973;