rs12703413

Variant names:

• chr7-141847047-G-A
• rs12703413

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 0.25 in 152,126 control chromosomes in the GnomAD database, including 5,608 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 0.25 (5608 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.137
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.67).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.445 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: 0.250 AC: 37990 AN: 152008 Hom.: 5608 Cov.: 32

Gnomad AFR AF: 0.0885

Gnomad AMI AF: 0.139

Gnomad AMR AF: 0.332

Gnomad ASJ AF: 0.312

Gnomad EAS AF: 0.461

Gnomad SAS AF: 0.300

Gnomad FIN AF: 0.278

Gnomad MID AF: 0.329

Gnomad NFE AF: 0.303

Gnomad OTH AF: 0.267

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

GnomAD4 genome AF: 0.250 AC: 37993 AN: 152126 Hom.: 5608 Cov.: 32 AF XY: 0.254 AC XY: 18865 AN XY: 74378

African (AFR) AF: 0.0885 AC: 3678 AN: 41536

American (AMR) AF: 0.332 AC: 5079 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.312 AC: 1083 AN: 3470

East Asian (EAS) AF: 0.460 AC: 2378 AN: 5168

South Asian (SAS) AF: 0.300 AC: 1447 AN: 4822

European-Finnish (FIN) AF: 0.278 AC: 2943 AN: 10586

Middle Eastern (MID) AF: 0.316 AC: 93 AN: 294

European-Non Finnish (NFE) AF: 0.303 AC: 20595 AN: 67944

Other (OTH) AF: 0.270 AC: 570 AN: 2108

Alfa AF: 0.291 Hom.: 8128

Bravo AF: 0.248

Asia WGS AF: 0.367 AC: 1273 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
CADD	Benign	9.8
DANN	Benign	0.91
PhyloP100		0.14

Splicing

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

Other links and lift over

dbSNP: rs12703413; hg19: chr7-141546847;