rs1642210

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr14-86981142-C-A
• chr14-86981142-C-G
• chr14-86981142-C-T

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

ENSG00000259061 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

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
ENSG00000259061	ENST00000554181.1	n.189-6846C>A		intron_variant	Intron 1 of 2	2

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

Gnomad4 AFR AF: 0.665

Gnomad4 AMR AF: 0.816

Gnomad4 ASJ AF: 0.932

Gnomad4 EAS AF: 0.790

Gnomad4 SAS AF: 0.910

Gnomad4 FIN AF: 0.979

Gnomad4 NFE AF: 0.958

Gnomad4 OTH AF: 0.882

Alfa AF: 0.929 Hom.: 28097

Bravo AF: 0.834

Asia WGS AF: 0.831 AC: 2891 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1642210; hg19: chr14-87447486;