1-110799868-C-T

Variant names:

• chr1-110799868-C-T
• rs343819

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 0.26 in 151,946 control chromosomes in the GnomAD database, including 5,276 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 0.26 (5276 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0350
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.262 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.260 AC: 39462 AN: 151828 Hom.: 5278 Cov.: 31

Gnomad AFR AF: 0.249

Gnomad AMI AF: 0.384

Gnomad AMR AF: 0.260

Gnomad ASJ AF: 0.373

Gnomad EAS AF: 0.105

Gnomad SAS AF: 0.230

Gnomad FIN AF: 0.304

Gnomad MID AF: 0.383

Gnomad NFE AF: 0.265

Gnomad OTH AF: 0.274

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

GnomAD4 genome AF: 0.260 AC: 39465 AN: 151946 Hom.: 5276 Cov.: 31 AF XY: 0.260 AC XY: 19340 AN XY: 74244

African (AFR) AF: 0.248 AC: 10284 AN: 41428

American (AMR) AF: 0.260 AC: 3963 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.373 AC: 1294 AN: 3468

East Asian (EAS) AF: 0.105 AC: 544 AN: 5168

South Asian (SAS) AF: 0.230 AC: 1106 AN: 4816

European-Finnish (FIN) AF: 0.304 AC: 3195 AN: 10524

Middle Eastern (MID) AF: 0.381 AC: 112 AN: 294

European-Non Finnish (NFE) AF: 0.265 AC: 18033 AN: 67960

Other (OTH) AF: 0.277 AC: 585 AN: 2110

Alfa AF: 0.262 Hom.: 21298

Bravo AF: 0.258

Asia WGS AF: 0.237 AC: 828 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.0
DANN	Benign	0.35
PhyloP100		0.035

Splicing

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

Other links and lift over

dbSNP: rs343819; hg19: chr1-111342490;