7-1249003-G-T

Variant names:

• chr7-1249003-G-T
• rs13241427

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 0.723 in 150,666 control chromosomes in the GnomAD database, including 39,981 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 0.72 (39981 hom., cov: 27)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.370
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.814 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: 0.723 AC: 108795 AN: 150548 Hom.: 39958 Cov.: 27

Gnomad AFR AF: 0.601

Gnomad AMI AF: 0.606

Gnomad AMR AF: 0.679

Gnomad ASJ AF: 0.769

Gnomad EAS AF: 0.659

Gnomad SAS AF: 0.835

Gnomad FIN AF: 0.789

Gnomad MID AF: 0.663

Gnomad NFE AF: 0.792

Gnomad OTH AF: 0.728

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

GnomAD4 genome AF: 0.723 AC: 108859 AN: 150666 Hom.: 39981 Cov.: 27 AF XY: 0.724 AC XY: 53262 AN XY: 73554

African (AFR) AF: 0.600 AC: 24580 AN: 40948

American (AMR) AF: 0.679 AC: 10289 AN: 15150

Ashkenazi Jewish (ASJ) AF: 0.769 AC: 2657 AN: 3454

East Asian (EAS) AF: 0.659 AC: 3346 AN: 5074

South Asian (SAS) AF: 0.836 AC: 3978 AN: 4760

European-Finnish (FIN) AF: 0.789 AC: 8215 AN: 10412

Middle Eastern (MID) AF: 0.648 AC: 188 AN: 290

European-Non Finnish (NFE) AF: 0.792 AC: 53553 AN: 67614

Other (OTH) AF: 0.730 AC: 1516 AN: 2078

Alfa AF: 0.768 Hom.: 170874

Bravo AF: 0.705

Asia WGS AF: 0.768 AC: 2673 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	4.8
DANN	Benign	0.30
PhyloP100		0.37

Splicing

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

Other links and lift over

dbSNP: rs13241427; hg19: chr7-1288639;