rs12735613

Positions:

• chr1-118341350-G-A
• chr1-118341350-G-C
• chr1-118341350-G-T

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 0.223 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.174

Gnomad4 AMR AF: 0.233

Gnomad4 ASJ AF: 0.298

Gnomad4 EAS AF: 0.285

Gnomad4 SAS AF: 0.299

Gnomad4 FIN AF: 0.236

Gnomad4 NFE AF: 0.236

Gnomad4 OTH AF: 0.211

Alfa AF: 0.234 Hom.: 6233

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12735613; hg19: chr1-118883973;