rs10502676

chr18-37667582-C-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, non coding transcript 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: ENST00000649194.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0990

Genes affected

(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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000649194.1	n.111-58262C>G		intron_variant, non_coding_transcript_variant

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;