rs343802

Positions:

• chr1-110774507-G-A
• chr1-110774507-G-C
• chr1-110774507-G-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.186 in 152,208 control chromosomes in the GnomAD database, including 3,284 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 0.19 (3284 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.87

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.31).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.236 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: 0.187 AC: 28395 AN: 152090 Hom.: 3287 Cov.: 32

Gnomad AFR AF: 0.0589

Gnomad AMI AF: 0.417

Gnomad AMR AF: 0.226

Gnomad ASJ AF: 0.380

Gnomad EAS AF: 0.127

Gnomad SAS AF: 0.188

Gnomad FIN AF: 0.231

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.239

Gnomad OTH AF: 0.221

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

GnomAD4 genome AF: 0.186 AC: 28382 AN: 152208 Hom.: 3284 Cov.: 32 AF XY: 0.188 AC XY: 13950 AN XY: 74394

Gnomad4 AFR AF: 0.0588

Gnomad4 AMR AF: 0.226

Gnomad4 ASJ AF: 0.380

Gnomad4 EAS AF: 0.127

Gnomad4 SAS AF: 0.187

Gnomad4 FIN AF: 0.231

Gnomad4 NFE AF: 0.239

Gnomad4 OTH AF: 0.224

Alfa AF: 0.200 Hom.: 1589

Bravo AF: 0.183

Asia WGS AF: 0.216 AC: 754 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.31
CADD	Benign	16
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: rs343802; hg19: chr1-111317129;