ENST00000649194.1:n.110+76277T>G

Variant names:

• chr18-37641667-T-G
• rs2217127
• ENST00000649194.1:n.110+76277T>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

Genes affected

ENSG00000285940 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000285940	ENST00000649194.1	n.110+76277T>G		intron_variant	Intron 1 of 8
ENSG00000305928	ENST00000814162.1	n.461+12281A>C		intron_variant	Intron 1 of 1

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

African (AFR) AF: 0.179 AC: 7426 AN: 41520

American (AMR) AF: 0.537 AC: 8186 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.617 AC: 2142 AN: 3470

East Asian (EAS) AF: 0.658 AC: 3399 AN: 5162

South Asian (SAS) AF: 0.527 AC: 2539 AN: 4816

European-Finnish (FIN) AF: 0.728 AC: 7697 AN: 10574

Middle Eastern (MID) AF: 0.534 AC: 157 AN: 294

European-Non Finnish (NFE) AF: 0.728 AC: 49511 AN: 68002

Other (OTH) AF: 0.602 AC: 1271 AN: 2110

Alfa AF: 0.656 Hom.: 106499

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
PhyloP100		0.19

Splicing

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

Other links and lift over

dbSNP: rs2217127; hg19: chr18-35221630;