chr14-86981142-C-A

Variant names:

• chr14-86981142-C-A
• rs1642210
• ENST00000554181.1:n.189-6846C>A

Variant summary

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

The ENST00000554181.1(ENSG00000259061):​n.189-6846C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.856 in 152,162 control chromosomes in the GnomAD database, including 57,048 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 0.86 (57048 hom., cov: 32)
• Consequence: ENSG00000259061 ENST00000554181.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.345
• Publications: 0 publications found

Genes affected

ENSG00000259061 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.952 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000554181.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000259061	ENST00000554181.1	TSL:2	n.189-6846C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.856 AC: 130201 AN: 152044 Hom.: 57025 Cov.: 32

Gnomad AFR AF: 0.665

Gnomad AMI AF: 0.948

Gnomad AMR AF: 0.816

Gnomad ASJ AF: 0.932

Gnomad EAS AF: 0.791

Gnomad SAS AF: 0.908

Gnomad FIN AF: 0.979

Gnomad MID AF: 0.915

Gnomad NFE AF: 0.958

Gnomad OTH AF: 0.880

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

GnomAD4 genome AF: 0.856 AC: 130269 AN: 152162 Hom.: 57048 Cov.: 32 AF XY: 0.856 AC XY: 63701 AN XY: 74420

African (AFR) AF: 0.665 AC: 27554 AN: 41444

American (AMR) AF: 0.816 AC: 12458 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.932 AC: 3234 AN: 3470

East Asian (EAS) AF: 0.790 AC: 4087 AN: 5172

South Asian (SAS) AF: 0.910 AC: 4393 AN: 4830

European-Finnish (FIN) AF: 0.979 AC: 10397 AN: 10622

Middle Eastern (MID) AF: 0.915 AC: 269 AN: 294

European-Non Finnish (NFE) AF: 0.958 AC: 65150 AN: 68030

Other (OTH) AF: 0.882 AC: 1864 AN: 2114

Alfa AF: 0.924 Hom.: 36463

Bravo AF: 0.834

Asia WGS AF: 0.831 AC: 2891 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	4.4
DANN	Benign	0.70
PhyloP100		0.34

Splicing

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

Other links and lift over

dbSNP: rs1642210; hg19: chr14-87447486;