7-101601694-C-A

Position:

• chr7-101601694-C-A

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 0.169 in 151,934 control chromosomes in the GnomAD database, including 2,215 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 0.17 (2215 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.07

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.188 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.169 AC: 25655 AN: 151816 Hom.: 2205 Cov.: 33

Gnomad AFR AF: 0.139

Gnomad AMI AF: 0.151

Gnomad AMR AF: 0.144

Gnomad ASJ AF: 0.160

Gnomad EAS AF: 0.159

Gnomad SAS AF: 0.195

Gnomad FIN AF: 0.177

Gnomad MID AF: 0.169

Gnomad NFE AF: 0.191

Gnomad OTH AF: 0.176

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

GnomAD4 genome AF: 0.169 AC: 25682 AN: 151934 Hom.: 2215 Cov.: 33 AF XY: 0.166 AC XY: 12337 AN XY: 74274

Gnomad4 AFR AF: 0.139

Gnomad4 AMR AF: 0.144

Gnomad4 ASJ AF: 0.160

Gnomad4 EAS AF: 0.158

Gnomad4 SAS AF: 0.194

Gnomad4 FIN AF: 0.177

Gnomad4 NFE AF: 0.191

Gnomad4 OTH AF: 0.179

Alfa AF: 0.187 Hom.: 1578

Bravo AF: 0.167

Asia WGS AF: 0.200 AC: 694 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.12
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17135662; hg19: chr7-101244974; COSMIC: COSV53499558;