chr17-40890629-C-A

Variant names:

• chr17-40890629-C-A
• rs2315504
• ENST00000818906.1:n.176-7327C>A

Variant summary

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

The ENST00000818906.1(ENSG00000265359):​n.176-7327C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.673 in 152,012 control chromosomes in the GnomAD database, including 35,822 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 0.67 (35822 hom., cov: 32)
• Consequence: ENSG00000265359 ENST00000818906.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.07
• Publications: 24 publications found

Genes affected

ENSG00000265359 (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 (EAS) allele frequency at 95% confidence interval = 0.96 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105371777	XR_934754.3	n.64-27600C>A		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000265359	ENST00000818906.1	n.176-7327C>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.672 AC: 102136 AN: 151896 Hom.: 35774 Cov.: 32

Gnomad AFR AF: 0.845

Gnomad AMI AF: 0.577

Gnomad AMR AF: 0.687

Gnomad ASJ AF: 0.587

Gnomad EAS AF: 0.983

Gnomad SAS AF: 0.669

Gnomad FIN AF: 0.645

Gnomad MID AF: 0.579

Gnomad NFE AF: 0.552

Gnomad OTH AF: 0.625

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

GnomAD4 genome AF: 0.673 AC: 102234 AN: 152012 Hom.: 35822 Cov.: 32 AF XY: 0.680 AC XY: 50520 AN XY: 74296

African (AFR) AF: 0.846 AC: 35058 AN: 41464

American (AMR) AF: 0.688 AC: 10503 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.587 AC: 2035 AN: 3468

East Asian (EAS) AF: 0.983 AC: 5101 AN: 5190

South Asian (SAS) AF: 0.668 AC: 3220 AN: 4818

European-Finnish (FIN) AF: 0.645 AC: 6789 AN: 10532

Middle Eastern (MID) AF: 0.571 AC: 168 AN: 294

European-Non Finnish (NFE) AF: 0.552 AC: 37523 AN: 67964

Other (OTH) AF: 0.624 AC: 1311 AN: 2102

Alfa AF: 0.591 Hom.: 74245

Bravo AF: 0.681

Asia WGS AF: 0.794 AC: 2761 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.057
DANN	Benign	0.40
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs2315504; hg19: chr17-39046881;