rs7092990

Variant names:

• chr10-71856778-C-T
• rs7092990

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 0.0758 in 152,212 control chromosomes in the GnomAD database, including 495 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 0.076 (495 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.299
• Publications: 1 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 (NFE) allele frequency at 95% confidence interval = 0.0935 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: 0.0759 AC: 11538 AN: 152094 Hom.: 495 Cov.: 32

Gnomad AFR AF: 0.0463

Gnomad AMI AF: 0.0439

Gnomad AMR AF: 0.0707

Gnomad ASJ AF: 0.169

Gnomad EAS AF: 0.00115

Gnomad SAS AF: 0.0826

Gnomad FIN AF: 0.0734

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.0955

Gnomad OTH AF: 0.0953

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

GnomAD4 genome AF: 0.0758 AC: 11536 AN: 152212 Hom.: 495 Cov.: 32 AF XY: 0.0750 AC XY: 5584 AN XY: 74430

African (AFR) AF: 0.0463 AC: 1922 AN: 41528

American (AMR) AF: 0.0706 AC: 1078 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.169 AC: 586 AN: 3466

East Asian (EAS) AF: 0.00116 AC: 6 AN: 5186

South Asian (SAS) AF: 0.0835 AC: 403 AN: 4826

European-Finnish (FIN) AF: 0.0734 AC: 779 AN: 10606

Middle Eastern (MID) AF: 0.0986 AC: 29 AN: 294

European-Non Finnish (NFE) AF: 0.0955 AC: 6494 AN: 68010

Other (OTH) AF: 0.0943 AC: 199 AN: 2110

Alfa AF: 0.0879 Hom.: 72

Bravo AF: 0.0741

Asia WGS AF: 0.0300 AC: 105 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	8.7
DANN	Benign	0.74
PhyloP100		0.30

Splicing

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

Other links and lift over

dbSNP: rs7092990; hg19: chr10-73616535;