rs17530068

Variant names:

• chr6-81483392-T-C
• rs17530068
• ENST00000759357.1:n.199+30337A>G

Variant summary

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

The ENST00000759357.1(ENSG00000298959):​n.199+30337A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.189 in 151,740 control chromosomes in the GnomAD database, including 3,285 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 0.19 (3285 hom., cov: 32)
• Consequence: ENSG00000298959 ENST00000759357.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0620
• Publications: 53 publications found

Genes affected

ENSG00000298959 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.237 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105377871	XR_007059658.1	n.23233+8099A>G		intron_variant	Intron 4 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000298959	ENST00000759357.1	n.199+30337A>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.189 AC: 28701 AN: 151622 Hom.: 3285 Cov.: 32

Gnomad AFR AF: 0.0607

Gnomad AMI AF: 0.239

Gnomad AMR AF: 0.243

Gnomad ASJ AF: 0.264

Gnomad EAS AF: 0.216

Gnomad SAS AF: 0.213

Gnomad FIN AF: 0.288

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.231

Gnomad OTH AF: 0.218

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

GnomAD4 genome AF: 0.189 AC: 28701 AN: 151740 Hom.: 3285 Cov.: 32 AF XY: 0.191 AC XY: 14190 AN XY: 74138

African (AFR) AF: 0.0606 AC: 2513 AN: 41498

American (AMR) AF: 0.243 AC: 3695 AN: 15190

Ashkenazi Jewish (ASJ) AF: 0.264 AC: 914 AN: 3462

East Asian (EAS) AF: 0.216 AC: 1106 AN: 5118

South Asian (SAS) AF: 0.213 AC: 1025 AN: 4816

European-Finnish (FIN) AF: 0.288 AC: 3040 AN: 10572

Middle Eastern (MID) AF: 0.197 AC: 58 AN: 294

European-Non Finnish (NFE) AF: 0.231 AC: 15676 AN: 67776

Other (OTH) AF: 0.217 AC: 456 AN: 2102

Alfa AF: 0.223 Hom.: 17221

Bravo AF: 0.182

Asia WGS AF: 0.199 AC: 690 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.4
DANN	Benign	0.51
PhyloP100		0.062

Splicing

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

Other links and lift over

dbSNP: rs17530068; hg19: chr6-82193109;