7-15024208-T-G

Variant names:

• chr7-15024208-T-G
• rs10244051

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 0.544 in 151,866 control chromosomes in the GnomAD database, including 22,775 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 0.54 (22775 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0360
• Publications: 27 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 (EAS) allele frequency at 95% confidence interval = 0.662 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: 0.544 AC: 82559 AN: 151748 Hom.: 22766 Cov.: 31

Gnomad AFR AF: 0.569

Gnomad AMI AF: 0.462

Gnomad AMR AF: 0.481

Gnomad ASJ AF: 0.554

Gnomad EAS AF: 0.681

Gnomad SAS AF: 0.637

Gnomad FIN AF: 0.440

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.543

Gnomad OTH AF: 0.532

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

GnomAD4 genome AF: 0.544 AC: 82612 AN: 151866 Hom.: 22775 Cov.: 31 AF XY: 0.540 AC XY: 40107 AN XY: 74222

African (AFR) AF: 0.569 AC: 23571 AN: 41420

American (AMR) AF: 0.481 AC: 7321 AN: 15222

Ashkenazi Jewish (ASJ) AF: 0.554 AC: 1922 AN: 3472

East Asian (EAS) AF: 0.681 AC: 3502 AN: 5144

South Asian (SAS) AF: 0.637 AC: 3060 AN: 4800

European-Finnish (FIN) AF: 0.440 AC: 4643 AN: 10558

Middle Eastern (MID) AF: 0.486 AC: 143 AN: 294

European-Non Finnish (NFE) AF: 0.543 AC: 36898 AN: 67940

Other (OTH) AF: 0.538 AC: 1132 AN: 2106

Alfa AF: 0.546 Hom.: 80620

Bravo AF: 0.544

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.5
DANN	Benign	0.69
PhyloP100		0.036

Splicing

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

Other links and lift over

dbSNP: rs10244051; hg19: chr7-15063833;