rs17109951

chr1-93442021-A-G

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 0.196 in 152,124 control chromosomes in the GnomAD database, including 5,113 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 0.20 (5113 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.384

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.461 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: 0.195 AC: 29673 AN: 152006 Hom.: 5092 Cov.: 32

Gnomad AFR AF: 0.466

Gnomad AMI AF: 0.0746

Gnomad AMR AF: 0.142

Gnomad ASJ AF: 0.0573

Gnomad EAS AF: 0.0655

Gnomad SAS AF: 0.101

Gnomad FIN AF: 0.113

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.0816

Gnomad OTH AF: 0.162

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

GnomAD4 genome AF: 0.196 AC: 29746 AN: 152124 Hom.: 5113 Cov.: 32 AF XY: 0.193 AC XY: 14359 AN XY: 74382

Gnomad4 AFR AF: 0.467

Gnomad4 AMR AF: 0.142

Gnomad4 ASJ AF: 0.0573

Gnomad4 EAS AF: 0.0658

Gnomad4 SAS AF: 0.100

Gnomad4 FIN AF: 0.113

Gnomad4 NFE AF: 0.0817

Gnomad4 OTH AF: 0.161

Alfa AF: 0.129 Hom.: 415

Bravo AF: 0.212

Asia WGS AF: 0.109 AC: 381 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
Cadd	Benign	5.5
Dann	Benign	0.91

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17109951; hg19: chr1-93907578;