14-100654937-T-C

Variant names:

• chr14-100654937-T-C
• rs1467537

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 0.586 in 152,104 control chromosomes in the GnomAD database, including 27,457 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 0.59 (27457 hom., cov: 35)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.74
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.691 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: 0.587 AC: 89159 AN: 151986 Hom.: 27452 Cov.: 35

Gnomad AFR AF: 0.494

Gnomad AMI AF: 0.725

Gnomad AMR AF: 0.496

Gnomad ASJ AF: 0.694

Gnomad EAS AF: 0.154

Gnomad SAS AF: 0.425

Gnomad FIN AF: 0.610

Gnomad MID AF: 0.713

Gnomad NFE AF: 0.696

Gnomad OTH AF: 0.593

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

GnomAD4 genome AF: 0.586 AC: 89180 AN: 152104 Hom.: 27457 Cov.: 35 AF XY: 0.576 AC XY: 42849 AN XY: 74370

African (AFR) AF: 0.493 AC: 20452 AN: 41496

American (AMR) AF: 0.495 AC: 7581 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.694 AC: 2407 AN: 3466

East Asian (EAS) AF: 0.155 AC: 796 AN: 5152

South Asian (SAS) AF: 0.427 AC: 2062 AN: 4826

European-Finnish (FIN) AF: 0.610 AC: 6461 AN: 10584

Middle Eastern (MID) AF: 0.719 AC: 210 AN: 292

European-Non Finnish (NFE) AF: 0.696 AC: 47316 AN: 67964

Other (OTH) AF: 0.586 AC: 1238 AN: 2112

Alfa AF: 0.640 Hom.: 3949

Bravo AF: 0.576

Asia WGS AF: 0.280 AC: 974 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.71
DANN	Benign	0.57
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs1467537; hg19: chr14-101121274;