rs17716275

Variant names:

• chr19-29086323-G-A
• rs17716275
• ENST00000656834.2:n.156-1757C>T

Variant summary

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

The ENST00000656834.2(ENSG00000288017):​n.156-1757C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0637 in 152,198 control chromosomes in the GnomAD database, including 387 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 0.064 (387 hom., cov: 33)
• Consequence: ENSG00000288017 ENST00000656834.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.596
• Publications: 3 publications found

Genes affected

ENSG00000288017 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.145 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000656834.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000288017	ENST00000656834.2		n.156-1757C>T		intron	N/A
	ENSG00000288017	ENST00000816732.1		n.46-1757C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0636 AC: 9676 AN: 152082 Hom.: 386 Cov.: 33

Gnomad AFR AF: 0.0793

Gnomad AMI AF: 0.0804

Gnomad AMR AF: 0.0499

Gnomad ASJ AF: 0.0349

Gnomad EAS AF: 0.152

Gnomad SAS AF: 0.155

Gnomad FIN AF: 0.0364

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.0491

Gnomad OTH AF: 0.0645

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

GnomAD4 genome AF: 0.0637 AC: 9690 AN: 152198 Hom.: 387 Cov.: 33 AF XY: 0.0657 AC XY: 4891 AN XY: 74408

African (AFR) AF: 0.0793 AC: 3293 AN: 41510

American (AMR) AF: 0.0499 AC: 763 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0349 AC: 121 AN: 3472

East Asian (EAS) AF: 0.153 AC: 788 AN: 5164

South Asian (SAS) AF: 0.154 AC: 742 AN: 4816

European-Finnish (FIN) AF: 0.0364 AC: 386 AN: 10610

Middle Eastern (MID) AF: 0.133 AC: 39 AN: 294

European-Non Finnish (NFE) AF: 0.0491 AC: 3341 AN: 68012

Other (OTH) AF: 0.0681 AC: 144 AN: 2114

Alfa AF: 0.0546 Hom.: 207

Bravo AF: 0.0642

Asia WGS AF: 0.158 AC: 553 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.7
DANN	Benign	0.41
PhyloP100		0.60

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs17716275; hg19: chr19-29577230;