rs12740035

Variant names:

• chr1-115012691-T-C
• rs12740035

Your query was ambiguous. Multiple possible variants found:

• chr1-115012691-T-C
• chr1-115012691-T-G

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 0.852 in 152,278 control chromosomes in the GnomAD database, including 55,317 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 0.85 (55317 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.40
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.07).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.964 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: 0.852 AC: 129639 AN: 152160 Hom.: 55275 Cov.: 34

Gnomad AFR AF: 0.836

Gnomad AMI AF: 0.852

Gnomad AMR AF: 0.875

Gnomad ASJ AF: 0.833

Gnomad EAS AF: 0.986

Gnomad SAS AF: 0.898

Gnomad FIN AF: 0.813

Gnomad MID AF: 0.804

Gnomad NFE AF: 0.851

Gnomad OTH AF: 0.828

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

GnomAD4 genome AF: 0.852 AC: 129738 AN: 152278 Hom.: 55317 Cov.: 34 AF XY: 0.852 AC XY: 63457 AN XY: 74458

African (AFR) AF: 0.836 AC: 34715 AN: 41538

American (AMR) AF: 0.876 AC: 13400 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.833 AC: 2889 AN: 3470

East Asian (EAS) AF: 0.986 AC: 5106 AN: 5178

South Asian (SAS) AF: 0.898 AC: 4337 AN: 4828

European-Finnish (FIN) AF: 0.813 AC: 8634 AN: 10614

Middle Eastern (MID) AF: 0.813 AC: 239 AN: 294

European-Non Finnish (NFE) AF: 0.851 AC: 57886 AN: 68026

Other (OTH) AF: 0.830 AC: 1755 AN: 2114

Alfa AF: 0.858 Hom.: 9084

Bravo AF: 0.858

Asia WGS AF: 0.947 AC: 3294 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.59
DANN	Benign	0.14
PhyloP100		-2.4

Splicing

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

Other links and lift over

dbSNP: rs12740035; hg19: chr1-115555312;