rs2167239

Variant names:

• chr14-87824961-G-A
• rs2167239
• ENST00000554305.5:n.111-8710C>T

Variant summary

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

The ENST00000554305.5(ENSG00000258807):​n.111-8710C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.172 in 151,982 control chromosomes in the GnomAD database, including 2,738 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 0.17 (2738 hom., cov: 32)
• Consequence: ENSG00000258807 ENST00000554305.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.221
• Publications: 6 publications found

Genes affected

ENSG00000258807 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.242 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
ENSG00000258807	ENST00000554305.5	n.111-8710C>T		intron_variant	Intron 2 of 6	5
ENSG00000259077	ENST00000555913.1	n.292+11281G>A		intron_variant	Intron 2 of 2	2

Frequencies

GnomAD3 genomes AF: 0.172 AC: 26117 AN: 151866 Hom.: 2740 Cov.: 32

Gnomad AFR AF: 0.0807

Gnomad AMI AF: 0.276

Gnomad AMR AF: 0.131

Gnomad ASJ AF: 0.125

Gnomad EAS AF: 0.00444

Gnomad SAS AF: 0.0974

Gnomad FIN AF: 0.244

Gnomad MID AF: 0.0924

Gnomad NFE AF: 0.245

Gnomad OTH AF: 0.174

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

GnomAD4 genome AF: 0.172 AC: 26105 AN: 151982 Hom.: 2738 Cov.: 32 AF XY: 0.168 AC XY: 12482 AN XY: 74268

African (AFR) AF: 0.0805 AC: 3340 AN: 41478

American (AMR) AF: 0.131 AC: 1999 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.125 AC: 433 AN: 3464

East Asian (EAS) AF: 0.00445 AC: 23 AN: 5166

South Asian (SAS) AF: 0.0969 AC: 466 AN: 4810

European-Finnish (FIN) AF: 0.244 AC: 2573 AN: 10532

Middle Eastern (MID) AF: 0.0925 AC: 27 AN: 292

European-Non Finnish (NFE) AF: 0.245 AC: 16628 AN: 67950

Other (OTH) AF: 0.173 AC: 364 AN: 2110

Alfa AF: 0.218 Hom.: 1950

Bravo AF: 0.159

Asia WGS AF: 0.0560 AC: 195 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.71
DANN	Benign	0.54
PhyloP100		-0.22
Mutation Taster		=60/40	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs2167239; hg19: chr14-88291305;