4-154889949-T-C

Variant names:

• chr4-154889949-T-C
• rs1343937

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 0.379 in 151,898 control chromosomes in the GnomAD database, including 12,395 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 0.38 (12395 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.204
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.559 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: 0.378 AC: 57435 AN: 151780 Hom.: 12365 Cov.: 31

Gnomad AFR AF: 0.565

Gnomad AMI AF: 0.268

Gnomad AMR AF: 0.363

Gnomad ASJ AF: 0.290

Gnomad EAS AF: 0.575

Gnomad SAS AF: 0.452

Gnomad FIN AF: 0.364

Gnomad MID AF: 0.329

Gnomad NFE AF: 0.257

Gnomad OTH AF: 0.365

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

GnomAD4 genome AF: 0.379 AC: 57526 AN: 151898 Hom.: 12395 Cov.: 31 AF XY: 0.387 AC XY: 28698 AN XY: 74200

African (AFR) AF: 0.566 AC: 23440 AN: 41446

American (AMR) AF: 0.362 AC: 5522 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.290 AC: 1007 AN: 3468

East Asian (EAS) AF: 0.576 AC: 2960 AN: 5140

South Asian (SAS) AF: 0.453 AC: 2182 AN: 4814

European-Finnish (FIN) AF: 0.364 AC: 3838 AN: 10534

Middle Eastern (MID) AF: 0.323 AC: 95 AN: 294

European-Non Finnish (NFE) AF: 0.257 AC: 17463 AN: 67934

Other (OTH) AF: 0.368 AC: 775 AN: 2108

Alfa AF: 0.299 Hom.: 20715

Bravo AF: 0.383

Asia WGS AF: 0.522 AC: 1810 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.1
DANN	Benign	0.84
PhyloP100		0.20

Splicing

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

Other links and lift over

dbSNP: rs1343937; hg19: chr4-155811101;