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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC112268194	XR_002958121.1	n.245-422A>C		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000310109	ENST00000847259.1	n.225-422A>C		intron_variant	Intron 1 of 2
ENSG00000310109	ENST00000847260.1	n.269-422A>C		intron_variant	Intron 1 of 1

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 v4.3

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

Other links and lift over

dbSNP: rs17760296; hg19: chr17-54615617;