rs17427680

Variant names:

• chr14-30340938-T-G
• rs17427680
• ENST00000820542.1:n.63-6121A>C

Variant summary

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

The ENST00000820542.1(ENSG00000306731):​n.63-6121A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0405 in 152,308 control chromosomes in the GnomAD database, including 147 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 0.041 (147 hom., cov: 32)
• Consequence: ENSG00000306731 ENST00000820542.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.38
• Publications: 1 publications found

Genes affected

ENSG00000306731 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.66).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0598 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000820542.1. 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
	ENSG00000306731	ENST00000820542.1		n.63-6121A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0406 AC: 6175 AN: 152190 Hom.: 147 Cov.: 32

Gnomad AFR AF: 0.0105

Gnomad AMI AF: 0.0186

Gnomad AMR AF: 0.0331

Gnomad ASJ AF: 0.0337

Gnomad EAS AF: 0.000577

Gnomad SAS AF: 0.0396

Gnomad FIN AF: 0.0588

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0614

Gnomad OTH AF: 0.0455

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

GnomAD4 genome AF: 0.0405 AC: 6175 AN: 152308 Hom.: 147 Cov.: 32 AF XY: 0.0413 AC XY: 3074 AN XY: 74478

African (AFR) AF: 0.0105 AC: 435 AN: 41580

American (AMR) AF: 0.0331 AC: 506 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0337 AC: 117 AN: 3472

East Asian (EAS) AF: 0.000578 AC: 3 AN: 5190

South Asian (SAS) AF: 0.0396 AC: 191 AN: 4820

European-Finnish (FIN) AF: 0.0588 AC: 624 AN: 10610

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.0614 AC: 4177 AN: 68026

Other (OTH) AF: 0.0450 AC: 95 AN: 2110

Alfa AF: 0.0384 Hom.: 55

Bravo AF: 0.0360

Asia WGS AF: 0.0140 AC: 50 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
CADD	Benign	9.7
DANN	Benign	0.84
PhyloP100		2.4

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: rs17427680;

hg19: chr14-30810144;