rs12600635

Variant names:

• chr17-17239582-A-G
• rs12600635
• ENST00000724562.1:n.48+1865A>G

Variant summary

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

The ENST00000724562.1(ENSG00000294588):​n.48+1865A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.148 in 152,220 control chromosomes in the GnomAD database, including 1,942 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 0.15 (1942 hom., cov: 33)
• Consequence: ENSG00000294588 ENST00000724562.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.170
• Publications: 25 publications found

Genes affected

ENSG00000294588 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.234 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000294588	ENST00000724562.1	n.48+1865A>G		intron_variant	Intron 1 of 2
ENSG00000294588	ENST00000724563.1	n.33-611A>G		intron_variant	Intron 1 of 3
ENSG00000294588	ENST00000724564.1	n.95+1802A>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.148 AC: 22492 AN: 152102 Hom.: 1939 Cov.: 33

Gnomad AFR AF: 0.0560

Gnomad AMI AF: 0.160

Gnomad AMR AF: 0.152

Gnomad ASJ AF: 0.209

Gnomad EAS AF: 0.219

Gnomad SAS AF: 0.243

Gnomad FIN AF: 0.141

Gnomad MID AF: 0.182

Gnomad NFE AF: 0.188

Gnomad OTH AF: 0.171

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

GnomAD4 genome AF: 0.148 AC: 22506 AN: 152220 Hom.: 1942 Cov.: 33 AF XY: 0.149 AC XY: 11086 AN XY: 74434

African (AFR) AF: 0.0560 AC: 2328 AN: 41550

American (AMR) AF: 0.152 AC: 2316 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.209 AC: 724 AN: 3472

East Asian (EAS) AF: 0.219 AC: 1134 AN: 5178

South Asian (SAS) AF: 0.245 AC: 1183 AN: 4826

European-Finnish (FIN) AF: 0.141 AC: 1497 AN: 10592

Middle Eastern (MID) AF: 0.182 AC: 53 AN: 292

European-Non Finnish (NFE) AF: 0.188 AC: 12760 AN: 68004

Other (OTH) AF: 0.173 AC: 365 AN: 2108

Alfa AF: 0.176 Hom.: 6941

Bravo AF: 0.146

Asia WGS AF: 0.188 AC: 654 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.2
DANN	Benign	0.53
PhyloP100		0.17

Splicing

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

Other links and lift over

dbSNP: rs12600635; hg19: chr17-17142896;