14-98021670-G-T

Variant names:

• chr14-98021670-G-T
• rs1456988

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 0.61 in 151,992 control chromosomes in the GnomAD database, including 29,518 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 0.61 (29518 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.109
• Publications: 27 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.712 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: 0.611 AC: 92734 AN: 151874 Hom.: 29511 Cov.: 32

Gnomad AFR AF: 0.441

Gnomad AMI AF: 0.825

Gnomad AMR AF: 0.652

Gnomad ASJ AF: 0.684

Gnomad EAS AF: 0.517

Gnomad SAS AF: 0.481

Gnomad FIN AF: 0.586

Gnomad MID AF: 0.684

Gnomad NFE AF: 0.717

Gnomad OTH AF: 0.622

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

GnomAD4 genome AF: 0.610 AC: 92774 AN: 151992 Hom.: 29518 Cov.: 32 AF XY: 0.601 AC XY: 44676 AN XY: 74292

African (AFR) AF: 0.441 AC: 18276 AN: 41442

American (AMR) AF: 0.651 AC: 9953 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.684 AC: 2374 AN: 3470

East Asian (EAS) AF: 0.517 AC: 2663 AN: 5148

South Asian (SAS) AF: 0.480 AC: 2314 AN: 4816

European-Finnish (FIN) AF: 0.586 AC: 6181 AN: 10550

Middle Eastern (MID) AF: 0.673 AC: 198 AN: 294

European-Non Finnish (NFE) AF: 0.717 AC: 48751 AN: 67970

Other (OTH) AF: 0.621 AC: 1312 AN: 2112

Alfa AF: 0.685 Hom.: 158357

Bravo AF: 0.612

Asia WGS AF: 0.505 AC: 1760 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	4.2
DANN	Benign	0.60
PhyloP100		0.11

Splicing

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

Other links and lift over

dbSNP: rs1456988; hg19: chr14-98488007;