rs1754162

Variant names:

• chr7-76633461-T-C
• rs1754162

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;