rs7072508

Variant names:

• chr10-121444843-A-T
• rs7072508

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 0.42 in 151,948 control chromosomes in the GnomAD database, including 14,296 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 0.42 (14296 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.41
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.515 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: 0.420 AC: 63757 AN: 151830 Hom.: 14284 Cov.: 32

Gnomad AFR AF: 0.315

Gnomad AMI AF: 0.431

Gnomad AMR AF: 0.524

Gnomad ASJ AF: 0.440

Gnomad EAS AF: 0.0548

Gnomad SAS AF: 0.285

Gnomad FIN AF: 0.510

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.482

Gnomad OTH AF: 0.443

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

GnomAD4 genome AF: 0.420 AC: 63785 AN: 151948 Hom.: 14296 Cov.: 32 AF XY: 0.419 AC XY: 31082 AN XY: 74264

African (AFR) AF: 0.314 AC: 13024 AN: 41430

American (AMR) AF: 0.524 AC: 7994 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.440 AC: 1527 AN: 3470

East Asian (EAS) AF: 0.0547 AC: 283 AN: 5170

South Asian (SAS) AF: 0.285 AC: 1373 AN: 4810

European-Finnish (FIN) AF: 0.510 AC: 5387 AN: 10558

Middle Eastern (MID) AF: 0.428 AC: 125 AN: 292

European-Non Finnish (NFE) AF: 0.482 AC: 32758 AN: 67950

Other (OTH) AF: 0.437 AC: 923 AN: 2110

Alfa AF: 0.440 Hom.: 1896

Bravo AF: 0.421

Asia WGS AF: 0.195 AC: 677 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.028
DANN	Benign	0.69
PhyloP100		-2.4

Splicing

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

Other links and lift over

dbSNP: rs7072508; hg19: chr10-123204357;