4-154613256-T-C

Variant names:

• chr4-154613256-T-C
• rs1800792

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 0.338 in 151,916 control chromosomes in the GnomAD database, including 9,880 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 0.34 (9880 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0180
• Publications: 20 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 = 0.446 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: 0.338 AC: 51292 AN: 151798 Hom.: 9887 Cov.: 31

Gnomad AFR AF: 0.154

Gnomad AMI AF: 0.392

Gnomad AMR AF: 0.311

Gnomad ASJ AF: 0.450

Gnomad EAS AF: 0.362

Gnomad SAS AF: 0.328

Gnomad FIN AF: 0.315

Gnomad MID AF: 0.472

Gnomad NFE AF: 0.450

Gnomad OTH AF: 0.385

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

GnomAD4 genome AF: 0.338 AC: 51285 AN: 151916 Hom.: 9880 Cov.: 31 AF XY: 0.331 AC XY: 24592 AN XY: 74236

African (AFR) AF: 0.153 AC: 6358 AN: 41452

American (AMR) AF: 0.311 AC: 4745 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.450 AC: 1559 AN: 3468

East Asian (EAS) AF: 0.362 AC: 1861 AN: 5136

South Asian (SAS) AF: 0.327 AC: 1571 AN: 4800

European-Finnish (FIN) AF: 0.315 AC: 3329 AN: 10572

Middle Eastern (MID) AF: 0.486 AC: 143 AN: 294

European-Non Finnish (NFE) AF: 0.450 AC: 30558 AN: 67924

Other (OTH) AF: 0.382 AC: 805 AN: 2110

Alfa AF: 0.422 Hom.: 59904

Bravo AF: 0.333

Asia WGS AF: 0.339 AC: 1177 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.8
DANN	Benign	0.46
PhyloP100		-0.018
PromoterAI		-0.010	Neutral

Splicing

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

Other links and lift over

dbSNP: rs1800792; hg19: chr4-155534408;