14-88360338-T-C

Variant names:

• chr14-88360338-T-C
• rs17124581

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 0.0722 in 152,272 control chromosomes in the GnomAD database, including 480 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 0.072 (480 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0900
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.238 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: 0.0722 AC: 10990 AN: 152154 Hom.: 484 Cov.: 33

Gnomad AFR AF: 0.0705

Gnomad AMI AF: 0.0186

Gnomad AMR AF: 0.112

Gnomad ASJ AF: 0.0372

Gnomad EAS AF: 0.250

Gnomad SAS AF: 0.122

Gnomad FIN AF: 0.0391

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0550

Gnomad OTH AF: 0.0664

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

GnomAD4 genome AF: 0.0722 AC: 10990 AN: 152272 Hom.: 480 Cov.: 33 AF XY: 0.0745 AC XY: 5545 AN XY: 74458

African (AFR) AF: 0.0705 AC: 2929 AN: 41568

American (AMR) AF: 0.112 AC: 1719 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0372 AC: 129 AN: 3472

East Asian (EAS) AF: 0.250 AC: 1291 AN: 5168

South Asian (SAS) AF: 0.122 AC: 588 AN: 4822

European-Finnish (FIN) AF: 0.0391 AC: 415 AN: 10612

Middle Eastern (MID) AF: 0.0714 AC: 21 AN: 294

European-Non Finnish (NFE) AF: 0.0550 AC: 3742 AN: 68012

Other (OTH) AF: 0.0658 AC: 139 AN: 2114

Alfa AF: 0.0661 Hom.: 2017

Bravo AF: 0.0779

Asia WGS AF: 0.165 AC: 574 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.0
DANN	Benign	0.40
PhyloP100		-0.090

Splicing

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

Other links and lift over

dbSNP: rs17124581; hg19: chr14-88826682;