rs10226084

Variant names:

• chr7-17957989-T-C
• rs10226084

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;