7-101642897-G-T

Variant names:

• chr7-101642897-G-T
• rs1722229

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 0.977 in 151,780 control chromosomes in the GnomAD database, including 72,515 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 0.98 (72515 hom., cov: 28)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.23
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.12).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.986 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: 0.977 AC: 148227 AN: 151662 Hom.: 72454 Cov.: 28

Gnomad AFR AF: 0.994

Gnomad AMI AF: 0.929

Gnomad AMR AF: 0.977

Gnomad ASJ AF: 0.942

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.989

Gnomad FIN AF: 0.973

Gnomad MID AF: 0.975

Gnomad NFE AF: 0.968

Gnomad OTH AF: 0.974

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

GnomAD4 genome AF: 0.977 AC: 148348 AN: 151780 Hom.: 72515 Cov.: 28 AF XY: 0.977 AC XY: 72451 AN XY: 74148

African (AFR) AF: 0.994 AC: 41126 AN: 41378

American (AMR) AF: 0.977 AC: 14805 AN: 15152

Ashkenazi Jewish (ASJ) AF: 0.942 AC: 3268 AN: 3468

East Asian (EAS) AF: 1.00 AC: 5156 AN: 5158

South Asian (SAS) AF: 0.990 AC: 4743 AN: 4792

European-Finnish (FIN) AF: 0.973 AC: 10268 AN: 10556

Middle Eastern (MID) AF: 0.973 AC: 286 AN: 294

European-Non Finnish (NFE) AF: 0.968 AC: 65808 AN: 67976

Other (OTH) AF: 0.975 AC: 2041 AN: 2094

Alfa AF: 0.971 Hom.: 3327

Bravo AF: 0.979

Asia WGS AF: 0.995 AC: 3459 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.090
DANN	Benign	0.33
PhyloP100		-4.2

Splicing

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

Other links and lift over

dbSNP: rs1722229; hg19: chr7-101286177;