17-27385939-G-A

Variant names:

• chr17-27385939-G-A
• rs4794888
• ENST00000728349.1:n.414-6348C>T

Variant summary

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

The ENST00000728349.1(ENSG00000295161):​n.414-6348C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.529 in 152,090 control chromosomes in the GnomAD database, including 21,553 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 0.53 (21553 hom., cov: 33)
• Consequence: ENSG00000295161 ENST00000728349.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.41
• Publications: 1 publications found

Genes affected

ENSG00000295161 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.673 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000728349.1. 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
	ENSG00000295161	ENST00000728349.1		n.414-6348C>T		intron	N/A
	ENSG00000295161	ENST00000728350.1		n.672-6348C>T		intron	N/A
	ENSG00000295161	ENST00000728351.1		n.189-6348C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.529 AC: 80417 AN: 151972 Hom.: 21535 Cov.: 33

Gnomad AFR AF: 0.476

Gnomad AMI AF: 0.596

Gnomad AMR AF: 0.478

Gnomad ASJ AF: 0.584

Gnomad EAS AF: 0.692

Gnomad SAS AF: 0.521

Gnomad FIN AF: 0.598

Gnomad MID AF: 0.620

Gnomad NFE AF: 0.546

Gnomad OTH AF: 0.540

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

GnomAD4 genome AF: 0.529 AC: 80479 AN: 152090 Hom.: 21553 Cov.: 33 AF XY: 0.531 AC XY: 39489 AN XY: 74350

African (AFR) AF: 0.476 AC: 19763 AN: 41510

American (AMR) AF: 0.478 AC: 7302 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.584 AC: 2024 AN: 3468

East Asian (EAS) AF: 0.691 AC: 3568 AN: 5160

South Asian (SAS) AF: 0.524 AC: 2521 AN: 4814

European-Finnish (FIN) AF: 0.598 AC: 6322 AN: 10570

Middle Eastern (MID) AF: 0.609 AC: 179 AN: 294

European-Non Finnish (NFE) AF: 0.546 AC: 37113 AN: 67962

Other (OTH) AF: 0.542 AC: 1145 AN: 2114

Alfa AF: 0.538 Hom.: 10628

Bravo AF: 0.519

Asia WGS AF: 0.577 AC: 2009 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	6.1
DANN	Benign	0.74
PhyloP100		1.4

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: rs4794888;

hg19: chr17-25712965;