rs10502676

Variant names:

• chr18-37667582-C-G
• rs10502676
• ENST00000649194.1:n.111-58262C>G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000649194.1(ENSG00000285940):​n.111-58262C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.161 in 152,092 control chromosomes in the GnomAD database, including 2,288 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 0.16 (2288 hom., cov: 32)
• Consequence: ENSG00000285940 ENST00000649194.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0990

Genes affected

ENSG00000285940 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.247 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
ENSG00000285940	ENST00000649194.1	n.111-58262C>G		intron_variant	Intron 1 of 8

Frequencies

GnomAD3 genomes AF: 0.161 AC: 24445 AN: 151974 Hom.: 2276 Cov.: 32

Gnomad AFR AF: 0.240

Gnomad AMI AF: 0.139

Gnomad AMR AF: 0.138

Gnomad ASJ AF: 0.210

Gnomad EAS AF: 0.0185

Gnomad SAS AF: 0.260

Gnomad FIN AF: 0.0987

Gnomad MID AF: 0.204

Gnomad NFE AF: 0.129

Gnomad OTH AF: 0.148

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

GnomAD4 genome AF: 0.161 AC: 24495 AN: 152092 Hom.: 2288 Cov.: 32 AF XY: 0.163 AC XY: 12135 AN XY: 74334

Gnomad4 AFR AF: 0.241

Gnomad4 AMR AF: 0.138

Gnomad4 ASJ AF: 0.210

Gnomad4 EAS AF: 0.0190

Gnomad4 SAS AF: 0.259

Gnomad4 FIN AF: 0.0987

Gnomad4 NFE AF: 0.129

Gnomad4 OTH AF: 0.147

Alfa AF: 0.147 Hom.: 238

Bravo AF: 0.164

Asia WGS AF: 0.167 AC: 584 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.8
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10502676; hg19: chr18-35247545;