rs2315504

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr17-40890629-C-A
• chr17-40890629-C-G
• chr17-40890629-C-T

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000818906.1. 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
	ENSG00000265359	ENST00000818906.1		n.176-7327C>A		intron	N/A

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2315504;

hg19: chr17-39046881;