rs17422551

chr1-79726638-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 0.0757 in 152,088 control chromosomes in the GnomAD database, including 578 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 0.076 (578 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.186

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.52).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.113 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: 0.0758 AC: 11518 AN: 151970 Hom.: 578 Cov.: 32

Gnomad AFR AF: 0.0207

Gnomad AMI AF: 0.102

Gnomad AMR AF: 0.0900

Gnomad ASJ AF: 0.115

Gnomad EAS AF: 0.000386

Gnomad SAS AF: 0.0322

Gnomad FIN AF: 0.0485

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.115

Gnomad OTH AF: 0.108

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

GnomAD4 genome AF: 0.0757 AC: 11509 AN: 152088 Hom.: 578 Cov.: 32 AF XY: 0.0716 AC XY: 5326 AN XY: 74340

Gnomad4 AFR AF: 0.0206

Gnomad4 AMR AF: 0.0899

Gnomad4 ASJ AF: 0.115

Gnomad4 EAS AF: 0.000386

Gnomad4 SAS AF: 0.0326

Gnomad4 FIN AF: 0.0485

Gnomad4 NFE AF: 0.115

Gnomad4 OTH AF: 0.107

Alfa AF: 0.0804 Hom.: 116

Bravo AF: 0.0797

Asia WGS AF: 0.0200 AC: 71 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.52
Cadd	Benign	2.6
Dann	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17422551; hg19: chr1-80192323;