chr7-22761034-G-T

Variant names:

• chr7-22761034-G-T
• rs10229203

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	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

African (AFR) AF: 0.157 AC: 6519 AN: 41518

American (AMR) AF: 0.0842 AC: 1287 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.196 AC: 680 AN: 3472

East Asian (EAS) AF: 0.000774 AC: 4 AN: 5166

South Asian (SAS) AF: 0.0938 AC: 453 AN: 4828

European-Finnish (FIN) AF: 0.101 AC: 1068 AN: 10602

Middle Eastern (MID) AF: 0.286 AC: 84 AN: 294

European-Non Finnish (NFE) AF: 0.0759 AC: 5159 AN: 68008

Other (OTH) AF: 0.121 AC: 257 AN: 2116

Alfa AF: 0.0916 Hom.: 2196

Bravo AF: 0.105

Asia WGS AF: 0.0440 AC: 154 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.6
DANN	Benign	0.47
PhyloP100		0.17

Splicing

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

Other links and lift over

dbSNP: rs10229203; hg19: chr7-22800653;