chr4-160183999-T-C

Variant names:

• chr4-160183999-T-C
• rs2349534

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 0.496 in 151,896 control chromosomes in the GnomAD database, including 19,145 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 0.50 (19145 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.14
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.59 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: 0.496 AC: 75292 AN: 151782 Hom.: 19114 Cov.: 31

Gnomad AFR AF: 0.596

Gnomad AMI AF: 0.489

Gnomad AMR AF: 0.531

Gnomad ASJ AF: 0.382

Gnomad EAS AF: 0.488

Gnomad SAS AF: 0.378

Gnomad FIN AF: 0.495

Gnomad MID AF: 0.315

Gnomad NFE AF: 0.444

Gnomad OTH AF: 0.457

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

GnomAD4 genome AF: 0.496 AC: 75372 AN: 151896 Hom.: 19145 Cov.: 31 AF XY: 0.495 AC XY: 36798 AN XY: 74266

African (AFR) AF: 0.596 AC: 24714 AN: 41432

American (AMR) AF: 0.531 AC: 8103 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.382 AC: 1325 AN: 3468

East Asian (EAS) AF: 0.488 AC: 2517 AN: 5160

South Asian (SAS) AF: 0.376 AC: 1812 AN: 4814

European-Finnish (FIN) AF: 0.495 AC: 5221 AN: 10548

Middle Eastern (MID) AF: 0.305 AC: 89 AN: 292

European-Non Finnish (NFE) AF: 0.444 AC: 30169 AN: 67920

Other (OTH) AF: 0.464 AC: 977 AN: 2104

Alfa AF: 0.459 Hom.: 2110

Bravo AF: 0.505

Asia WGS AF: 0.490 AC: 1702 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	7.6
DANN	Benign	0.46
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs2349534; hg19: chr4-161105151;