rs7091573

Variant names:

• chr10-2021612-T-C
• rs7091573

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.383 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

Gnomad4 AFR AF: 0.301

Gnomad4 AMR AF: 0.366

Gnomad4 ASJ AF: 0.409

Gnomad4 EAS AF: 0.416

Gnomad4 SAS AF: 0.471

Gnomad4 FIN AF: 0.433

Gnomad4 NFE AF: 0.421

Gnomad4 OTH AF: 0.383

Alfa AF: 0.410 Hom.: 7933

Bravo AF: 0.371

Asia WGS AF: 0.378 AC: 1316 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7091573; hg19: chr10-2063806;