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. The variant received -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
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.0491 AC: 2037 AN: 41500

American (AMR) AF: 0.184 AC: 2806 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.355 AC: 1231 AN: 3468

East Asian (EAS) AF: 0.0133 AC: 69 AN: 5182

South Asian (SAS) AF: 0.0840 AC: 405 AN: 4824

European-Finnish (FIN) AF: 0.162 AC: 1710 AN: 10536

Middle Eastern (MID) AF: 0.207 AC: 61 AN: 294

European-Non Finnish (NFE) AF: 0.265 AC: 17971 AN: 67820

Other (OTH) AF: 0.208 AC: 439 AN: 2108

Alfa AF: 0.242 Hom.: 7528

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
PhyloP100		0.54

Splicing

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

Other links and lift over

dbSNP: rs12740489; hg19: chr1-97296935;