7-22761034-G-T

Variant names:

• chr7-22761034-G-T
• rs10229203

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 0.102 in 152,208 control chromosomes in the GnomAD database, including 976 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 0.10 (976 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.165

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.154 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: 0.102 AC: 15523 AN: 152090 Hom.: 975 Cov.: 32

Gnomad AFR AF: 0.157

Gnomad AMI AF: 0.0417

Gnomad AMR AF: 0.0842

Gnomad ASJ AF: 0.196

Gnomad EAS AF: 0.000772

Gnomad SAS AF: 0.0925

Gnomad FIN AF: 0.101

Gnomad MID AF: 0.301

Gnomad NFE AF: 0.0758

Gnomad OTH AF: 0.123

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

GnomAD4 genome AF: 0.102 AC: 15549 AN: 152208 Hom.: 976 Cov.: 32 AF XY: 0.102 AC XY: 7625 AN XY: 74406

Gnomad4 AFR AF: 0.157

Gnomad4 AMR AF: 0.0842

Gnomad4 ASJ AF: 0.196

Gnomad4 EAS AF: 0.000774

Gnomad4 SAS AF: 0.0938

Gnomad4 FIN AF: 0.101

Gnomad4 NFE AF: 0.0759

Gnomad4 OTH AF: 0.121

Alfa AF: 0.0867 Hom.: 1406

Bravo AF: 0.105

Asia WGS AF: 0.0440 AC: 154 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.6
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10229203; hg19: chr7-22800653;