14-42150058-G-C

Variant names:

• chr14-42150058-G-C
• rs1954627
• ENST00000836359.1:n.253-25G>C

Variant summary

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

The ENST00000836359.1(ENSG00000308787):​n.253-25G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.737 in 152,018 control chromosomes in the GnomAD database, including 41,336 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 0.74 (41336 hom., cov: 32)
• Consequence: ENSG00000308787 ENST00000836359.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.11
• Publications: 3 publications found

Genes affected

ENSG00000308787 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.858 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000836359.1. 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
	ENSG00000308787	ENST00000836359.1		n.253-25G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.737 AC: 111971 AN: 151900 Hom.: 41303 Cov.: 32

Gnomad AFR AF: 0.736

Gnomad AMI AF: 0.579

Gnomad AMR AF: 0.739

Gnomad ASJ AF: 0.643

Gnomad EAS AF: 0.879

Gnomad SAS AF: 0.737

Gnomad FIN AF: 0.782

Gnomad MID AF: 0.704

Gnomad NFE AF: 0.727

Gnomad OTH AF: 0.731

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

GnomAD4 genome AF: 0.737 AC: 112063 AN: 152018 Hom.: 41336 Cov.: 32 AF XY: 0.740 AC XY: 55003 AN XY: 74302

African (AFR) AF: 0.736 AC: 30534 AN: 41478

American (AMR) AF: 0.739 AC: 11262 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.643 AC: 2233 AN: 3472

East Asian (EAS) AF: 0.880 AC: 4549 AN: 5172

South Asian (SAS) AF: 0.736 AC: 3553 AN: 4828

European-Finnish (FIN) AF: 0.782 AC: 8276 AN: 10586

Middle Eastern (MID) AF: 0.705 AC: 206 AN: 292

European-Non Finnish (NFE) AF: 0.727 AC: 49372 AN: 67930

Other (OTH) AF: 0.735 AC: 1550 AN: 2110

Alfa AF: 0.726 Hom.: 4715

Bravo AF: 0.733

Asia WGS AF: 0.790 AC: 2746 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.46
DANN	Benign	0.33
PhyloP100		-2.1

Splicing

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

Other links and lift over

dbSNP: rs1954627; hg19: chr14-42619261;