rs7090512

Positions:

• chr10-6068866-C-T

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 0.659 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.579

Gnomad4 AMR AF: 0.676

Gnomad4 ASJ AF: 0.548

Gnomad4 EAS AF: 0.697

Gnomad4 SAS AF: 0.713

Gnomad4 FIN AF: 0.732

Gnomad4 NFE AF: 0.693

Gnomad4 OTH AF: 0.628

Alfa AF: 0.674 Hom.: 52296

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7090512; hg19: chr10-6110829;