14-98671130-C-T

Variant names:

• chr14-98671130-C-T
• rs1950475

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 0.386 in 151,948 control chromosomes in the GnomAD database, including 11,356 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 0.39 (11356 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.278
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.428 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: 0.386 AC: 58618 AN: 151828 Hom.: 11340 Cov.: 32

Gnomad AFR AF: 0.368

Gnomad AMI AF: 0.445

Gnomad AMR AF: 0.399

Gnomad ASJ AF: 0.397

Gnomad EAS AF: 0.344

Gnomad SAS AF: 0.444

Gnomad FIN AF: 0.400

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.389

Gnomad OTH AF: 0.407

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

GnomAD4 genome AF: 0.386 AC: 58670 AN: 151948 Hom.: 11356 Cov.: 32 AF XY: 0.389 AC XY: 28875 AN XY: 74288

African (AFR) AF: 0.368 AC: 15258 AN: 41444

American (AMR) AF: 0.400 AC: 6101 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.397 AC: 1378 AN: 3468

East Asian (EAS) AF: 0.344 AC: 1769 AN: 5148

South Asian (SAS) AF: 0.444 AC: 2138 AN: 4814

European-Finnish (FIN) AF: 0.400 AC: 4225 AN: 10564

Middle Eastern (MID) AF: 0.349 AC: 102 AN: 292

European-Non Finnish (NFE) AF: 0.389 AC: 26432 AN: 67924

Other (OTH) AF: 0.407 AC: 861 AN: 2116

Alfa AF: 0.302 Hom.: 1105

Bravo AF: 0.384

Asia WGS AF: 0.439 AC: 1525 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.6
DANN	Benign	0.85
PhyloP100		-0.28

Splicing

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

Other links and lift over

dbSNP: rs1950475; hg19: chr14-99137467;