rs12740489

Variant names:

• chr1-96831379-G-A
• rs12740489

Your query was ambiguous. Multiple possible variants found:

• chr1-96831379-G-A
• chr1-96831379-G-C
• chr1-96831379-G-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.178 in 151,896 control chromosomes in the GnomAD database, including 3,196 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 0.18 (3196 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.541

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.35).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.262 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: 0.178 AC: 26979 AN: 151780 Hom.: 3201 Cov.: 32

Gnomad AFR AF: 0.0493

Gnomad AMI AF: 0.262

Gnomad AMR AF: 0.184

Gnomad ASJ AF: 0.355

Gnomad EAS AF: 0.0133

Gnomad SAS AF: 0.0843

Gnomad FIN AF: 0.162

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.265

Gnomad OTH AF: 0.210

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

GnomAD4 genome AF: 0.178 AC: 26968 AN: 151896 Hom.: 3196 Cov.: 32 AF XY: 0.169 AC XY: 12566 AN XY: 74210

Gnomad4 AFR AF: 0.0491

Gnomad4 AMR AF: 0.184

Gnomad4 ASJ AF: 0.355

Gnomad4 EAS AF: 0.0133

Gnomad4 SAS AF: 0.0840

Gnomad4 FIN AF: 0.162

Gnomad4 NFE AF: 0.265

Gnomad4 OTH AF: 0.208

Alfa AF: 0.243 Hom.: 6416

Bravo AF: 0.176

Asia WGS AF: 0.0590 AC: 206 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.35
CADD	Benign	17
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12740489; hg19: chr1-97296935;