rs10226084

Positions:

• chr7-17957989-T-C

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 0.458 in 151,968 control chromosomes in the GnomAD database, including 16,420 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 0.46 (16420 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.415

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.499 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: 0.458 AC: 69581 AN: 151854 Hom.: 16401 Cov.: 32

Gnomad AFR AF: 0.384

Gnomad AMI AF: 0.457

Gnomad AMR AF: 0.508

Gnomad ASJ AF: 0.413

Gnomad EAS AF: 0.329

Gnomad SAS AF: 0.295

Gnomad FIN AF: 0.616

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.492

Gnomad OTH AF: 0.460

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

GnomAD4 genome AF: 0.458 AC: 69649 AN: 151968 Hom.: 16420 Cov.: 32 AF XY: 0.462 AC XY: 34333 AN XY: 74272

Gnomad4 AFR AF: 0.384

Gnomad4 AMR AF: 0.508

Gnomad4 ASJ AF: 0.413

Gnomad4 EAS AF: 0.329

Gnomad4 SAS AF: 0.294

Gnomad4 FIN AF: 0.616

Gnomad4 NFE AF: 0.492

Gnomad4 OTH AF: 0.457

Alfa AF: 0.304 Hom.: 848

Bravo AF: 0.451

Asia WGS AF: 0.318 AC: 1106 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	0.97
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10226084; hg19: chr7-17997612;