18-61739905-A-G

Variant names:

• chr18-61739905-A-G
• rs1984372
• ENST00000590199.6:n.537+8135T>C

Variant summary

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

The ENST00000590199.6(ENSG00000267175):​n.537+8135T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.436 in 151,990 control chromosomes in the GnomAD database, including 14,612 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 0.44 (14612 hom., cov: 31)
• Consequence: ENSG00000267175 ENST00000590199.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.382
• Publications: 2 publications found

Genes affected

ENSG00000267175 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.46 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
ENSG00000267175	ENST00000590199.6	n.537+8135T>C		intron_variant	Intron 2 of 3	3
ENSG00000267175	ENST00000590968.1	n.233+8170T>C		intron_variant	Intron 2 of 3	2

Frequencies

GnomAD3 genomes AF: 0.436 AC: 66269 AN: 151870 Hom.: 14599 Cov.: 31

Gnomad AFR AF: 0.381

Gnomad AMI AF: 0.480

Gnomad AMR AF: 0.425

Gnomad ASJ AF: 0.448

Gnomad EAS AF: 0.442

Gnomad SAS AF: 0.478

Gnomad FIN AF: 0.503

Gnomad MID AF: 0.361

Gnomad NFE AF: 0.458

Gnomad OTH AF: 0.453

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

GnomAD4 genome AF: 0.436 AC: 66325 AN: 151990 Hom.: 14612 Cov.: 31 AF XY: 0.441 AC XY: 32750 AN XY: 74300

African (AFR) AF: 0.381 AC: 15786 AN: 41432

American (AMR) AF: 0.424 AC: 6484 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.448 AC: 1554 AN: 3472

East Asian (EAS) AF: 0.442 AC: 2272 AN: 5146

South Asian (SAS) AF: 0.477 AC: 2295 AN: 4814

European-Finnish (FIN) AF: 0.503 AC: 5319 AN: 10582

Middle Eastern (MID) AF: 0.371 AC: 109 AN: 294

European-Non Finnish (NFE) AF: 0.458 AC: 31104 AN: 67954

Other (OTH) AF: 0.457 AC: 965 AN: 2110

Alfa AF: 0.387 Hom.: 2090

Bravo AF: 0.430

Asia WGS AF: 0.514 AC: 1790 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	4.0
DANN	Benign	0.26
PhyloP100		0.38

Splicing

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

Other links and lift over

dbSNP: rs1984372; hg19: chr18-59407138;