rs7083969

Variant names:

• chr10-106236415-G-A
• rs7083969

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 0.374 in 151,076 control chromosomes in the GnomAD database, including 11,962 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 0.37 (11962 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.13

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.494 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: 0.374 AC: 56473 AN: 150956 Hom.: 11954 Cov.: 31

Gnomad AFR AF: 0.500

Gnomad AMI AF: 0.316

Gnomad AMR AF: 0.355

Gnomad ASJ AF: 0.329

Gnomad EAS AF: 0.505

Gnomad SAS AF: 0.487

Gnomad FIN AF: 0.304

Gnomad MID AF: 0.290

Gnomad NFE AF: 0.298

Gnomad OTH AF: 0.377

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

GnomAD4 genome AF: 0.374 AC: 56518 AN: 151076 Hom.: 11962 Cov.: 31 AF XY: 0.376 AC XY: 27717 AN XY: 73792

Gnomad4 AFR AF: 0.500

Gnomad4 AMR AF: 0.354

Gnomad4 ASJ AF: 0.329

Gnomad4 EAS AF: 0.505

Gnomad4 SAS AF: 0.487

Gnomad4 FIN AF: 0.304

Gnomad4 NFE AF: 0.298

Gnomad4 OTH AF: 0.376

Alfa AF: 0.321 Hom.: 9608

Bravo AF: 0.381

Asia WGS AF: 0.482 AC: 1673 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.097
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: rs7083969; hg19: chr10-107996173;