rs7091573

Variant names:

• chr10-2021612-T-C
• rs7091573

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 0.383 in 152,086 control chromosomes in the GnomAD database, including 11,405 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 0.38 (11405 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.04
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.455 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.383 AC: 58210 AN: 151968 Hom.: 11401 Cov.: 32

Gnomad AFR AF: 0.301

Gnomad AMI AF: 0.266

Gnomad AMR AF: 0.366

Gnomad ASJ AF: 0.409

Gnomad EAS AF: 0.417

Gnomad SAS AF: 0.471

Gnomad FIN AF: 0.433

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.421

Gnomad OTH AF: 0.384

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

GnomAD4 genome AF: 0.383 AC: 58240 AN: 152086 Hom.: 11405 Cov.: 32 AF XY: 0.386 AC XY: 28705 AN XY: 74330

African (AFR) AF: 0.301 AC: 12477 AN: 41490

American (AMR) AF: 0.366 AC: 5585 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.409 AC: 1420 AN: 3468

East Asian (EAS) AF: 0.416 AC: 2150 AN: 5166

South Asian (SAS) AF: 0.471 AC: 2269 AN: 4818

European-Finnish (FIN) AF: 0.433 AC: 4576 AN: 10568

Middle Eastern (MID) AF: 0.364 AC: 107 AN: 294

European-Non Finnish (NFE) AF: 0.421 AC: 28604 AN: 67982

Other (OTH) AF: 0.383 AC: 809 AN: 2112

Alfa AF: 0.409 Hom.: 10697

Bravo AF: 0.371

Asia WGS AF: 0.378 AC: 1316 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.51
DANN	Benign	0.22
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs7091573; hg19: chr10-2063806;