4-115275150-A-T

Variant names:

• chr4-115275150-A-T
• rs13144478

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 0.0548 in 152,162 control chromosomes in the GnomAD database, including 341 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 0.055 (341 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.48
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0785 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: 0.0549 AC: 8340 AN: 152046 Hom.: 341 Cov.: 32

Gnomad AFR AF: 0.0131

Gnomad AMI AF: 0.232

Gnomad AMR AF: 0.0283

Gnomad ASJ AF: 0.0406

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.0288

Gnomad FIN AF: 0.123

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0803

Gnomad OTH AF: 0.0465

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

GnomAD4 genome AF: 0.0548 AC: 8335 AN: 152162 Hom.: 341 Cov.: 32 AF XY: 0.0556 AC XY: 4133 AN XY: 74392

African (AFR) AF: 0.0130 AC: 541 AN: 41574

American (AMR) AF: 0.0282 AC: 431 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0406 AC: 141 AN: 3470

East Asian (EAS) AF: 0.000386 AC: 2 AN: 5182

South Asian (SAS) AF: 0.0290 AC: 140 AN: 4830

European-Finnish (FIN) AF: 0.123 AC: 1304 AN: 10576

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.0803 AC: 5453 AN: 67936

Other (OTH) AF: 0.0460 AC: 97 AN: 2110

Alfa AF: 0.0339 Hom.: 26

Bravo AF: 0.0467

Asia WGS AF: 0.0110 AC: 39 AN: 3448

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.4
DANN	Benign	0.49
PhyloP100		1.5

Splicing

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

Other links and lift over

dbSNP: rs13144478; hg19: chr4-116196306;