rs1958208

Variant names:

• chr14-81658696-G-A
• rs1958208
• ENST00000721834.1:n.126+3895C>T

Your query was ambiguous. Multiple possible variants found:

• chr14-81658696-G-A
• chr14-81658696-G-C
• chr14-81658696-G-T

Variant summary

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

The ENST00000721834.1(ENSG00000294195):​n.126+3895C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.687 in 151,938 control chromosomes in the GnomAD database, including 36,055 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 0.69 (36055 hom., cov: 31)
• Consequence: ENSG00000294195 ENST00000721834.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.167
• Publications: 2 publications found

Genes affected

ENSG00000294195 (HGNC:):

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 = 0.755 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
ENSG00000294195	ENST00000721834.1	n.126+3895C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.687 AC: 104272 AN: 151820 Hom.: 36022 Cov.: 31

Gnomad AFR AF: 0.761

Gnomad AMI AF: 0.515

Gnomad AMR AF: 0.648

Gnomad ASJ AF: 0.684

Gnomad EAS AF: 0.775

Gnomad SAS AF: 0.706

Gnomad FIN AF: 0.548

Gnomad MID AF: 0.747

Gnomad NFE AF: 0.666

Gnomad OTH AF: 0.683

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

GnomAD4 genome AF: 0.687 AC: 104362 AN: 151938 Hom.: 36055 Cov.: 31 AF XY: 0.682 AC XY: 50625 AN XY: 74256

African (AFR) AF: 0.762 AC: 31584 AN: 41464

American (AMR) AF: 0.648 AC: 9884 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.684 AC: 2372 AN: 3470

East Asian (EAS) AF: 0.775 AC: 4004 AN: 5168

South Asian (SAS) AF: 0.706 AC: 3394 AN: 4810

European-Finnish (FIN) AF: 0.548 AC: 5749 AN: 10498

Middle Eastern (MID) AF: 0.745 AC: 219 AN: 294

European-Non Finnish (NFE) AF: 0.666 AC: 45251 AN: 67952

Other (OTH) AF: 0.681 AC: 1436 AN: 2108

Alfa AF: 0.563 Hom.: 1651

Bravo AF: 0.697

Asia WGS AF: 0.741 AC: 2580 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	0.88
DANN	Benign	0.63
PhyloP100		-0.17

Splicing

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

Other links and lift over

dbSNP: rs1958208; hg19: chr14-82125040;