rs17763685

Variant names:

• chr8-24998990-C-T
• rs17763685
• ENST00000522570.1:n.349+6640C>T

Variant summary

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

The ENST00000522570.1(ENSG00000253832):​n.349+6640C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0925 in 152,092 control chromosomes in the GnomAD database, including 748 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 0.093 (748 hom., cov: 31)
• Consequence: ENSG00000253832 ENST00000522570.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.491
• Publications: 2 publications found

Genes affected

ENSG00000253832 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.115 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000522570.1. 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
	ENSG00000253832	ENST00000522570.1	TSL:3	n.349+6640C>T		intron	N/A
	ENSG00000253832	ENST00000814715.1		n.90-9404C>T		intron	N/A
	ENSG00000253832	ENST00000814716.1		n.78-9404C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0926 AC: 14073 AN: 151974 Hom.: 750 Cov.: 31

Gnomad AFR AF: 0.0534

Gnomad AMI AF: 0.0857

Gnomad AMR AF: 0.0875

Gnomad ASJ AF: 0.101

Gnomad EAS AF: 0.0204

Gnomad SAS AF: 0.0793

Gnomad FIN AF: 0.136

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.117

Gnomad OTH AF: 0.0967

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

GnomAD4 genome AF: 0.0925 AC: 14073 AN: 152092 Hom.: 748 Cov.: 31 AF XY: 0.0921 AC XY: 6850 AN XY: 74366

African (AFR) AF: 0.0534 AC: 2215 AN: 41484

American (AMR) AF: 0.0874 AC: 1335 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.101 AC: 351 AN: 3466

East Asian (EAS) AF: 0.0199 AC: 103 AN: 5174

South Asian (SAS) AF: 0.0793 AC: 383 AN: 4828

European-Finnish (FIN) AF: 0.136 AC: 1438 AN: 10568

Middle Eastern (MID) AF: 0.0884 AC: 26 AN: 294

European-Non Finnish (NFE) AF: 0.117 AC: 7942 AN: 67980

Other (OTH) AF: 0.0957 AC: 202 AN: 2110

Alfa AF: 0.105 Hom.: 1573

Bravo AF: 0.0855

Asia WGS AF: 0.0550 AC: 191 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.8
DANN	Benign	0.53
PhyloP100		-0.49

Splicing

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

Other links and lift over

dbSNP: rs17763685; hg19: chr8-24856504;