chr4-110663263-C-T

Variant names:

• chr4-110663263-C-T
• rs12498374

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 0.159 in 152,032 control chromosomes in the GnomAD database, including 2,390 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 0.16 (2390 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.830
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.29 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: 0.159 AC: 24176 AN: 151916 Hom.: 2388 Cov.: 32

Gnomad AFR AF: 0.0525

Gnomad AMI AF: 0.0844

Gnomad AMR AF: 0.142

Gnomad ASJ AF: 0.162

Gnomad EAS AF: 0.302

Gnomad SAS AF: 0.139

Gnomad FIN AF: 0.217

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.210

Gnomad OTH AF: 0.161

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

GnomAD4 genome AF: 0.159 AC: 24170 AN: 152032 Hom.: 2390 Cov.: 32 AF XY: 0.162 AC XY: 12018 AN XY: 74286

African (AFR) AF: 0.0524 AC: 2174 AN: 41476

American (AMR) AF: 0.142 AC: 2169 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.162 AC: 562 AN: 3470

East Asian (EAS) AF: 0.303 AC: 1563 AN: 5164

South Asian (SAS) AF: 0.138 AC: 666 AN: 4826

European-Finnish (FIN) AF: 0.217 AC: 2287 AN: 10528

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.210 AC: 14306 AN: 67972

Other (OTH) AF: 0.159 AC: 336 AN: 2110

Alfa AF: 0.185 Hom.: 3583

Bravo AF: 0.148

Asia WGS AF: 0.196 AC: 683 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	5.3
DANN	Benign	0.51
PhyloP100		0.83

Splicing

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

Other links and lift over

dbSNP: rs12498374; hg19: chr4-111584419;