chr18-37641667-T-G

Position:

• chr18-37641667-T-G

Variant summary

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

The ENST00000649194.1(ENSG00000285940):​n.110+76277T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.546 in 152,100 control chromosomes in the GnomAD database, including 26,913 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 0.55 (26913 hom., cov: 33)
• Consequence: ENSG00000285940 ENST00000649194.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.194

Genes affected

ENSG00000285940 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.723 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000285940	ENST00000649194.1	n.110+76277T>G		intron_variant

Frequencies

GnomAD3 genomes AF: 0.546 AC: 82979 AN: 151982 Hom.: 26909 Cov.: 33

Gnomad AFR AF: 0.179

Gnomad AMI AF: 0.724

Gnomad AMR AF: 0.537

Gnomad ASJ AF: 0.617

Gnomad EAS AF: 0.658

Gnomad SAS AF: 0.525

Gnomad FIN AF: 0.728

Gnomad MID AF: 0.525

Gnomad NFE AF: 0.728

Gnomad OTH AF: 0.607

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

GnomAD4 genome AF: 0.546 AC: 82985 AN: 152100 Hom.: 26913 Cov.: 33 AF XY: 0.544 AC XY: 40413 AN XY: 74316

Gnomad4 AFR AF: 0.179

Gnomad4 AMR AF: 0.537

Gnomad4 ASJ AF: 0.617

Gnomad4 EAS AF: 0.658

Gnomad4 SAS AF: 0.527

Gnomad4 FIN AF: 0.728

Gnomad4 NFE AF: 0.728

Gnomad4 OTH AF: 0.602

Alfa AF: 0.691 Hom.: 73741

Bravo AF: 0.516

Asia WGS AF: 0.541 AC: 1878 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	5.6
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2217127; hg19: chr18-35221630;