chr4-114154887-T-A

Variant names:

• chr4-114154887-T-A
• rs1112494

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 0.389 in 152,126 control chromosomes in the GnomAD database, including 12,221 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 0.39 (12221 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0150
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.69).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.488 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: 0.389 AC: 59196 AN: 152008 Hom.: 12208 Cov.: 33

Gnomad AFR AF: 0.270

Gnomad AMI AF: 0.304

Gnomad AMR AF: 0.497

Gnomad ASJ AF: 0.362

Gnomad EAS AF: 0.358

Gnomad SAS AF: 0.376

Gnomad FIN AF: 0.474

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.431

Gnomad OTH AF: 0.392

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

GnomAD4 genome AF: 0.389 AC: 59228 AN: 152126 Hom.: 12221 Cov.: 33 AF XY: 0.393 AC XY: 29215 AN XY: 74354

African (AFR) AF: 0.270 AC: 11210 AN: 41528

American (AMR) AF: 0.497 AC: 7587 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.362 AC: 1256 AN: 3470

East Asian (EAS) AF: 0.358 AC: 1855 AN: 5178

South Asian (SAS) AF: 0.379 AC: 1825 AN: 4820

European-Finnish (FIN) AF: 0.474 AC: 5013 AN: 10566

Middle Eastern (MID) AF: 0.316 AC: 93 AN: 294

European-Non Finnish (NFE) AF: 0.431 AC: 29292 AN: 67978

Other (OTH) AF: 0.388 AC: 820 AN: 2114

Alfa AF: 0.411 Hom.: 1657

Bravo AF: 0.389

Asia WGS AF: 0.340 AC: 1182 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
CADD	Benign	7.0
DANN	Benign	0.80
PhyloP100		0.015

Splicing

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

Other links and lift over

dbSNP: rs1112494; hg19: chr4-115076043;