4-110818000-C-T

Variant names:

• chr4-110818000-C-T
• rs13130446

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 0.417 in 151,636 control chromosomes in the GnomAD database, including 14,480 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 0.42 (14480 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.983
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.503 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: 0.417 AC: 63174 AN: 151522 Hom.: 14474 Cov.: 32

Gnomad AFR AF: 0.205

Gnomad AMI AF: 0.404

Gnomad AMR AF: 0.472

Gnomad ASJ AF: 0.419

Gnomad EAS AF: 0.509

Gnomad SAS AF: 0.486

Gnomad FIN AF: 0.513

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.508

Gnomad OTH AF: 0.398

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

GnomAD4 genome AF: 0.417 AC: 63190 AN: 151636 Hom.: 14480 Cov.: 32 AF XY: 0.421 AC XY: 31172 AN XY: 74088

African (AFR) AF: 0.205 AC: 8490 AN: 41428

American (AMR) AF: 0.472 AC: 7159 AN: 15166

Ashkenazi Jewish (ASJ) AF: 0.419 AC: 1451 AN: 3466

East Asian (EAS) AF: 0.510 AC: 2624 AN: 5150

South Asian (SAS) AF: 0.486 AC: 2340 AN: 4812

European-Finnish (FIN) AF: 0.513 AC: 5412 AN: 10546

Middle Eastern (MID) AF: 0.397 AC: 116 AN: 292

European-Non Finnish (NFE) AF: 0.508 AC: 34400 AN: 67760

Other (OTH) AF: 0.394 AC: 830 AN: 2104

Alfa AF: 0.480 Hom.: 76788

Bravo AF: 0.402

Asia WGS AF: 0.449 AC: 1558 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.55
DANN	Benign	0.37
PhyloP100		-0.98

Splicing

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

Other links and lift over

dbSNP: rs13130446; hg19: chr4-111739156;