rs17760296

Variant names:

• chr17-56538256-T-G
• rs17760296
• ENST00000847259.1:n.225-422A>C

Variant summary

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

The ENST00000847259.1(ENSG00000310109):​n.225-422A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.121 in 152,296 control chromosomes in the GnomAD database, including 1,455 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 0.12 (1455 hom., cov: 33)
• Consequence: ENSG00000310109 ENST00000847259.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0640
• Publications: 13 publications found

Genes affected

ENSG00000310109 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.159 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000847259.1. 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
	ENSG00000310109	ENST00000847259.1		n.225-422A>C		intron	N/A
	ENSG00000310109	ENST00000847260.1		n.269-422A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.121 AC: 18366 AN: 152178 Hom.: 1457 Cov.: 33

Gnomad AFR AF: 0.0480

Gnomad AMI AF: 0.120

Gnomad AMR AF: 0.0845

Gnomad ASJ AF: 0.122

Gnomad EAS AF: 0.0163

Gnomad SAS AF: 0.0613

Gnomad FIN AF: 0.267

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.162

Gnomad OTH AF: 0.141

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

GnomAD4 genome AF: 0.121 AC: 18356 AN: 152296 Hom.: 1455 Cov.: 33 AF XY: 0.123 AC XY: 9144 AN XY: 74476

African (AFR) AF: 0.0479 AC: 1990 AN: 41576

American (AMR) AF: 0.0845 AC: 1292 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.122 AC: 422 AN: 3468

East Asian (EAS) AF: 0.0164 AC: 85 AN: 5190

South Asian (SAS) AF: 0.0613 AC: 296 AN: 4826

European-Finnish (FIN) AF: 0.267 AC: 2837 AN: 10614

Middle Eastern (MID) AF: 0.170 AC: 50 AN: 294

European-Non Finnish (NFE) AF: 0.161 AC: 10981 AN: 68012

Other (OTH) AF: 0.139 AC: 294 AN: 2110

Alfa AF: 0.141 Hom.: 7508

Bravo AF: 0.103

Asia WGS AF: 0.0420 AC: 148 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	3.9
DANN	Benign	0.62
PhyloP100		0.064

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: rs17760296;

hg19: chr17-54615617;