chr17-70025996-G-T

Variant names:

• chr17-70025996-G-T
• rs180156
• ENST00000435112.5:n.307-3799C>A

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000435112.5(ENSG00000230258):​n.307-3799C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.828 in 152,192 control chromosomes in the GnomAD database, including 52,251 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 0.83 (52251 hom., cov: 33)
• Consequence: ENSG00000230258 ENST00000435112.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.548
• Publications: 1 publications found

Genes affected

ENSG00000230258 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.42).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.858 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000435112.5. 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
	ENSG00000230258	ENST00000435112.5	TSL:3	n.307-3799C>A		intron	N/A
	ENSG00000230258	ENST00000587325.1	TSL:3	n.319-3799C>A		intron	N/A
	ENSG00000230258	ENST00000807092.1		n.577-3799C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.828 AC: 125955 AN: 152074 Hom.: 52224 Cov.: 33

Gnomad AFR AF: 0.794

Gnomad AMI AF: 0.825

Gnomad AMR AF: 0.800

Gnomad ASJ AF: 0.891

Gnomad EAS AF: 0.839

Gnomad SAS AF: 0.881

Gnomad FIN AF: 0.911

Gnomad MID AF: 0.829

Gnomad NFE AF: 0.835

Gnomad OTH AF: 0.815

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

GnomAD4 genome AF: 0.828 AC: 126029 AN: 152192 Hom.: 52251 Cov.: 33 AF XY: 0.831 AC XY: 61871 AN XY: 74422

African (AFR) AF: 0.794 AC: 32949 AN: 41510

American (AMR) AF: 0.800 AC: 12238 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.891 AC: 3092 AN: 3472

East Asian (EAS) AF: 0.839 AC: 4345 AN: 5178

South Asian (SAS) AF: 0.880 AC: 4246 AN: 4826

European-Finnish (FIN) AF: 0.911 AC: 9663 AN: 10610

Middle Eastern (MID) AF: 0.840 AC: 247 AN: 294

European-Non Finnish (NFE) AF: 0.835 AC: 56783 AN: 67984

Other (OTH) AF: 0.810 AC: 1715 AN: 2116

Alfa AF: 0.836 Hom.: 6623

Bravo AF: 0.818

Asia WGS AF: 0.848 AC: 2951 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.42
CADD	Benign	9.0
DANN	Benign	0.95
PhyloP100		-0.55

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: rs180156;

hg19: chr17-68022137;