14-83972417-C-T

Variant names:

• chr14-83972417-C-T
• rs2210185
• XM_047432045.1:c.100-934G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XM_047432045.1(LOC124903401):​c.100-934G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.516 in 151,768 control chromosomes in the GnomAD database, including 20,648 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 0.52 (20648 hom., cov: 32)
• Consequence: LOC124903401 XM_047432045.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.481
• Publications: 0 publications found

Genes affected

LOC124903401 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.557 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124903401	XM_047432045.1	c.100-934G>A		intron_variant	Intron 1 of 3		XP_047288001.1
LOC124903401	XR_007064377.1	n.170+2317G>A		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.515 AC: 78165 AN: 151650 Hom.: 20618 Cov.: 32

Gnomad AFR AF: 0.541

Gnomad AMI AF: 0.533

Gnomad AMR AF: 0.535

Gnomad ASJ AF: 0.454

Gnomad EAS AF: 0.355

Gnomad SAS AF: 0.574

Gnomad FIN AF: 0.410

Gnomad MID AF: 0.548

Gnomad NFE AF: 0.522

Gnomad OTH AF: 0.550

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

GnomAD4 genome AF: 0.516 AC: 78255 AN: 151768 Hom.: 20648 Cov.: 32 AF XY: 0.510 AC XY: 37878 AN XY: 74218

African (AFR) AF: 0.541 AC: 22315 AN: 41248

American (AMR) AF: 0.536 AC: 8165 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.454 AC: 1575 AN: 3472

East Asian (EAS) AF: 0.355 AC: 1833 AN: 5162

South Asian (SAS) AF: 0.574 AC: 2769 AN: 4820

European-Finnish (FIN) AF: 0.410 AC: 4322 AN: 10550

Middle Eastern (MID) AF: 0.558 AC: 163 AN: 292

European-Non Finnish (NFE) AF: 0.522 AC: 35469 AN: 67962

Other (OTH) AF: 0.550 AC: 1159 AN: 2106

Alfa AF: 0.517 Hom.: 7411

Bravo AF: 0.529

Asia WGS AF: 0.492 AC: 1709 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.51
DANN	Benign	0.55
PhyloP100		-0.48

Splicing

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

Other links and lift over

dbSNP: rs2210185; hg19: chr14-84438761;