rs1754162

chr7-76633461-T-C

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 0.166 in 130,390 control chromosomes in the GnomAD database, including 3,339 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 (3339 hom., cov: 19)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: No conservation score assigned

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.223 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: 0.166 AC: 21634 AN: 130290 Hom.: 3333 Cov.: 19

Gnomad AFR AF: 0.0908

Gnomad AMI AF: 0.290

Gnomad AMR AF: 0.153

Gnomad ASJ AF: 0.245

Gnomad EAS AF: 0.0461

Gnomad SAS AF: 0.182

Gnomad FIN AF: 0.126

Gnomad MID AF: 0.273

Gnomad NFE AF: 0.226

Gnomad OTH AF: 0.196

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

GnomAD4 genome AF: 0.166 AC: 21645 AN: 130390 Hom.: 3339 Cov.: 19 AF XY: 0.163 AC XY: 10251 AN XY: 62932

Gnomad4 AFR AF: 0.0906

Gnomad4 AMR AF: 0.152

Gnomad4 ASJ AF: 0.245

Gnomad4 EAS AF: 0.0464

Gnomad4 SAS AF: 0.184

Gnomad4 FIN AF: 0.126

Gnomad4 NFE AF: 0.226

Gnomad4 OTH AF: 0.195

Alfa AF: 0.202 Hom.: 670

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	5.7
Dann	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1754162; hg19: chr7-76262778;