rs17422551

Variant names:

• chr1-79726638-G-T
• rs17422551

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 0.0757 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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.0206 AC: 857 AN: 41522

American (AMR) AF: 0.0899 AC: 1369 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.115 AC: 400 AN: 3470

East Asian (EAS) AF: 0.000386 AC: 2 AN: 5176

South Asian (SAS) AF: 0.0326 AC: 157 AN: 4812

European-Finnish (FIN) AF: 0.0485 AC: 513 AN: 10588

Middle Eastern (MID) AF: 0.160 AC: 47 AN: 294

European-Non Finnish (NFE) AF: 0.115 AC: 7845 AN: 67968

Other (OTH) AF: 0.107 AC: 226 AN: 2112

Alfa AF: 0.0755 Hom.: 355

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
PhyloP100		0.19

Splicing

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

Other links and lift over

dbSNP: rs17422551; hg19: chr1-80192323;