rs10229457

Positions:

• chr7-22761181-G-A
• chr7-22761181-G-C
• chr7-22761181-G-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 0.444 in 152,060 control chromosomes in the GnomAD database, including 18,178 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 0.44 (18178 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.720

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.917 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: 0.444 AC: 67451 AN: 151942 Hom.: 18137 Cov.: 32

Gnomad AFR AF: 0.654

Gnomad AMI AF: 0.262

Gnomad AMR AF: 0.548

Gnomad ASJ AF: 0.501

Gnomad EAS AF: 0.939

Gnomad SAS AF: 0.622

Gnomad FIN AF: 0.211

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.277

Gnomad OTH AF: 0.473

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

GnomAD4 genome AF: 0.444 AC: 67551 AN: 152060 Hom.: 18178 Cov.: 32 AF XY: 0.451 AC XY: 33489 AN XY: 74330

Gnomad4 AFR AF: 0.654

Gnomad4 AMR AF: 0.549

Gnomad4 ASJ AF: 0.501

Gnomad4 EAS AF: 0.939

Gnomad4 SAS AF: 0.622

Gnomad4 FIN AF: 0.211

Gnomad4 NFE AF: 0.277

Gnomad4 OTH AF: 0.479

Alfa AF: 0.339 Hom.: 5697

Bravo AF: 0.478

Asia WGS AF: 0.778 AC: 2701 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	7.1
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10229457; hg19: chr7-22800800;