rs4981158

Variant names:

• chr14-20359638-T-C
• rs4981158

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 0.302 in 151,844 control chromosomes in the GnomAD database, including 7,199 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 0.30 (7199 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.39
• Publications: 11 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.365 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: 0.302 AC: 45810 AN: 151728 Hom.: 7184 Cov.: 32

Gnomad AFR AF: 0.369

Gnomad AMI AF: 0.191

Gnomad AMR AF: 0.239

Gnomad ASJ AF: 0.232

Gnomad EAS AF: 0.279

Gnomad SAS AF: 0.378

Gnomad FIN AF: 0.291

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.279

Gnomad OTH AF: 0.279

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

GnomAD4 genome AF: 0.302 AC: 45870 AN: 151844 Hom.: 7199 Cov.: 32 AF XY: 0.301 AC XY: 22315 AN XY: 74164

African (AFR) AF: 0.369 AC: 15306 AN: 41424

American (AMR) AF: 0.239 AC: 3643 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.232 AC: 805 AN: 3470

East Asian (EAS) AF: 0.279 AC: 1445 AN: 5172

South Asian (SAS) AF: 0.379 AC: 1829 AN: 4830

European-Finnish (FIN) AF: 0.291 AC: 3036 AN: 10438

Middle Eastern (MID) AF: 0.248 AC: 73 AN: 294

European-Non Finnish (NFE) AF: 0.279 AC: 18970 AN: 67936

Other (OTH) AF: 0.279 AC: 589 AN: 2110

Alfa AF: 0.302 Hom.: 2159

Bravo AF: 0.299

Asia WGS AF: 0.334 AC: 1162 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.81
DANN	Benign	0.46
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs4981158; hg19: chr14-20827797;