rs7090512

Variant names:

• chr10-6068866-C-T
• rs7090512

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 0.659 in 152,036 control chromosomes in the GnomAD database, including 33,437 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 0.66 (33437 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.97
• Publications: 33 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.693 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: 0.659 AC: 100161 AN: 151918 Hom.: 33413 Cov.: 31

Gnomad AFR AF: 0.579

Gnomad AMI AF: 0.718

Gnomad AMR AF: 0.676

Gnomad ASJ AF: 0.548

Gnomad EAS AF: 0.698

Gnomad SAS AF: 0.712

Gnomad FIN AF: 0.732

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.693

Gnomad OTH AF: 0.629

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

GnomAD4 genome AF: 0.659 AC: 100227 AN: 152036 Hom.: 33437 Cov.: 31 AF XY: 0.661 AC XY: 49170 AN XY: 74338

African (AFR) AF: 0.579 AC: 23983 AN: 41406

American (AMR) AF: 0.676 AC: 10345 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.548 AC: 1902 AN: 3472

East Asian (EAS) AF: 0.697 AC: 3604 AN: 5168

South Asian (SAS) AF: 0.713 AC: 3442 AN: 4826

European-Finnish (FIN) AF: 0.732 AC: 7741 AN: 10574

Middle Eastern (MID) AF: 0.520 AC: 153 AN: 294

European-Non Finnish (NFE) AF: 0.693 AC: 47076 AN: 67970

Other (OTH) AF: 0.628 AC: 1328 AN: 2114

Alfa AF: 0.668 Hom.: 82329

Bravo AF: 0.650

Asia WGS AF: 0.712 AC: 2480 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.015
DANN	Benign	0.56
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs7090512; hg19: chr10-6110829;