7-22761034-G-T

Position:

• chr7-22761034-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 0.102 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;