ENST00000756734.1:n.96+35278G>A

Variant names:

• chr18-71467426-G-A
• rs17288584
• ENST00000756734.1:n.96+35278G>A

Variant summary

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

The ENST00000756734.1(ENSG00000298599):​n.96+35278G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.036 in 152,184 control chromosomes in the GnomAD database, including 157 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 0.036 (157 hom., cov: 32)
• Consequence: ENSG00000298599 ENST00000756734.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.268
• Publications: 1 publications found

Genes affected

ENSG00000298599 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0558 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000756734.1. 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
	ENSG00000298599	ENST00000756734.1		n.96+35278G>A		intron	N/A
	ENSG00000298599	ENST00000756735.1		n.52+35278G>A		intron	N/A
	ENSG00000298599	ENST00000756736.1		n.134+35278G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0360 AC: 5478 AN: 152068 Hom.: 157 Cov.: 32

Gnomad AFR AF: 0.00845

Gnomad AMI AF: 0.0132

Gnomad AMR AF: 0.0195

Gnomad ASJ AF: 0.0228

Gnomad EAS AF: 0.000770

Gnomad SAS AF: 0.0275

Gnomad FIN AF: 0.0608

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.0573

Gnomad OTH AF: 0.0272

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

GnomAD4 genome AF: 0.0360 AC: 5475 AN: 152184 Hom.: 157 Cov.: 32 AF XY: 0.0350 AC XY: 2604 AN XY: 74390

African (AFR) AF: 0.00843 AC: 350 AN: 41524

American (AMR) AF: 0.0194 AC: 297 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.0228 AC: 79 AN: 3468

East Asian (EAS) AF: 0.000772 AC: 4 AN: 5182

South Asian (SAS) AF: 0.0274 AC: 132 AN: 4822

European-Finnish (FIN) AF: 0.0608 AC: 643 AN: 10580

Middle Eastern (MID) AF: 0.0136 AC: 4 AN: 294

European-Non Finnish (NFE) AF: 0.0573 AC: 3897 AN: 68014

Other (OTH) AF: 0.0269 AC: 57 AN: 2116

Alfa AF: 0.0483 Hom.: 354

Bravo AF: 0.0318

Asia WGS AF: 0.0110 AC: 37 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.25
DANN	Benign	0.60
PhyloP100		-0.27

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: rs17288584;

hg19: chr18-69134662;