rs7083969

Positions:

• chr10-106236415-G-A

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;