chr1-93442021-A-G

Variant names:

• chr1-93442021-A-G
• rs17109951

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 0.196 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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.467 AC: 19349 AN: 41452

American (AMR) AF: 0.142 AC: 2167 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0573 AC: 199 AN: 3472

East Asian (EAS) AF: 0.0658 AC: 342 AN: 5194

South Asian (SAS) AF: 0.100 AC: 483 AN: 4812

European-Finnish (FIN) AF: 0.113 AC: 1195 AN: 10584

Middle Eastern (MID) AF: 0.167 AC: 49 AN: 294

European-Non Finnish (NFE) AF: 0.0817 AC: 5553 AN: 67998

Other (OTH) AF: 0.161 AC: 341 AN: 2114

Alfa AF: 0.138 Hom.: 927

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
PhyloP100		0.38

Splicing

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

Other links and lift over

dbSNP: rs17109951; hg19: chr1-93907578;