18-44105760-T-G

Variant names:

• chr18-44105760-T-G
• rs6507566
• ENST00000750746.1:n.723-19938T>G

Variant summary

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

The ENST00000750746.1(ENSG00000297742):​n.723-19938T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.687 in 151,988 control chromosomes in the GnomAD database, including 36,186 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 0.69 (36186 hom., cov: 31)
• Consequence: ENSG00000297742 ENST00000750746.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.77
• Publications: 1 publications found

Genes affected

ENSG00000297742 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.88 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
ENSG00000297742	ENST00000750746.1	n.723-19938T>G		intron_variant	Intron 6 of 6

Frequencies

GnomAD3 genomes AF: 0.687 AC: 104382 AN: 151870 Hom.: 36145 Cov.: 31

Gnomad AFR AF: 0.649

Gnomad AMI AF: 0.534

Gnomad AMR AF: 0.786

Gnomad ASJ AF: 0.665

Gnomad EAS AF: 0.901

Gnomad SAS AF: 0.730

Gnomad FIN AF: 0.696

Gnomad MID AF: 0.835

Gnomad NFE AF: 0.670

Gnomad OTH AF: 0.698

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

GnomAD4 genome AF: 0.687 AC: 104471 AN: 151988 Hom.: 36186 Cov.: 31 AF XY: 0.692 AC XY: 51419 AN XY: 74252

African (AFR) AF: 0.649 AC: 26900 AN: 41422

American (AMR) AF: 0.787 AC: 12022 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.665 AC: 2308 AN: 3470

East Asian (EAS) AF: 0.901 AC: 4649 AN: 5158

South Asian (SAS) AF: 0.730 AC: 3511 AN: 4812

European-Finnish (FIN) AF: 0.696 AC: 7341 AN: 10550

Middle Eastern (MID) AF: 0.823 AC: 242 AN: 294

European-Non Finnish (NFE) AF: 0.670 AC: 45529 AN: 67978

Other (OTH) AF: 0.702 AC: 1483 AN: 2114

Alfa AF: 0.672 Hom.: 4893

Bravo AF: 0.694

Asia WGS AF: 0.773 AC: 2688 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.1
DANN	Benign	0.70
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs6507566; hg19: chr18-41685725;