14-20793574-C-T

Variant names:

• chr14-20793574-C-T
• rs10131141
• ENST00000796740.1:n.78+6330G>A

Variant summary

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

The ENST00000796740.1(ENSG00000303727):​n.78+6330G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.627 in 151,962 control chromosomes in the GnomAD database, including 29,986 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 0.63 (29986 hom., cov: 31)
• Consequence: ENSG00000303727 ENST00000796740.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.75
• Publications: 4 publications found

Genes affected

ENSG00000303727 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.744 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000796740.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000303727	ENST00000796740.1		n.78+6330G>A		intron	N/A
	ENSG00000303727	ENST00000796741.1		n.71+6330G>A		intron	N/A
	ENSG00000303727	ENST00000796742.1		n.64+6330G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.627 AC: 95209 AN: 151844 Hom.: 29947 Cov.: 31

Gnomad AFR AF: 0.629

Gnomad AMI AF: 0.679

Gnomad AMR AF: 0.672

Gnomad ASJ AF: 0.627

Gnomad EAS AF: 0.764

Gnomad SAS AF: 0.742

Gnomad FIN AF: 0.574

Gnomad MID AF: 0.655

Gnomad NFE AF: 0.604

Gnomad OTH AF: 0.635

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

GnomAD4 genome AF: 0.627 AC: 95300 AN: 151962 Hom.: 29986 Cov.: 31 AF XY: 0.629 AC XY: 46741 AN XY: 74278

African (AFR) AF: 0.629 AC: 26056 AN: 41426

American (AMR) AF: 0.673 AC: 10277 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.627 AC: 2173 AN: 3468

East Asian (EAS) AF: 0.764 AC: 3951 AN: 5174

South Asian (SAS) AF: 0.741 AC: 3570 AN: 4816

European-Finnish (FIN) AF: 0.574 AC: 6050 AN: 10542

Middle Eastern (MID) AF: 0.656 AC: 193 AN: 294

European-Non Finnish (NFE) AF: 0.604 AC: 41066 AN: 67948

Other (OTH) AF: 0.639 AC: 1350 AN: 2114

Alfa AF: 0.614 Hom.: 72383

Bravo AF: 0.632

Asia WGS AF: 0.763 AC: 2653 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.15
DANN	Benign	0.16
PhyloP100		-3.8

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs10131141;

hg19: chr14-21261733;