18-31731071-G-A

Variant names:

• chr18-31731071-G-A
• rs985492
• ENST00000693320.2:n.1118+5750G>A

Variant summary

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

The ENST00000693320.2(ENSG00000293306):​n.1118+5750G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.538 in 151,980 control chromosomes in the GnomAD database, including 22,055 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 0.54 (22055 hom., cov: 32)
• Consequence: ENSG00000293306 ENST00000693320.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.928
• Publications: 7 publications found

Genes affected

ENSG00000293306 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.546 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
ENSG00000293306	ENST00000693320.2	n.1118+5750G>A		intron_variant	Intron 1 of 1
ENSG00000293306	ENST00000723809.1	n.999+5647G>A		intron_variant	Intron 1 of 2
ENSG00000293306	ENST00000723810.1	n.1016+5647G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.538 AC: 81645 AN: 151862 Hom.: 22035 Cov.: 32

Gnomad AFR AF: 0.539

Gnomad AMI AF: 0.626

Gnomad AMR AF: 0.557

Gnomad ASJ AF: 0.428

Gnomad EAS AF: 0.540

Gnomad SAS AF: 0.558

Gnomad FIN AF: 0.566

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.532

Gnomad OTH AF: 0.512

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

GnomAD4 genome AF: 0.538 AC: 81717 AN: 151980 Hom.: 22055 Cov.: 32 AF XY: 0.540 AC XY: 40102 AN XY: 74264

African (AFR) AF: 0.540 AC: 22364 AN: 41440

American (AMR) AF: 0.556 AC: 8495 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.428 AC: 1482 AN: 3466

East Asian (EAS) AF: 0.540 AC: 2787 AN: 5164

South Asian (SAS) AF: 0.559 AC: 2693 AN: 4816

European-Finnish (FIN) AF: 0.566 AC: 5967 AN: 10544

Middle Eastern (MID) AF: 0.445 AC: 130 AN: 292

European-Non Finnish (NFE) AF: 0.532 AC: 36146 AN: 67962

Other (OTH) AF: 0.512 AC: 1083 AN: 2114

Alfa AF: 0.523 Hom.: 66916

Bravo AF: 0.535

Asia WGS AF: 0.539 AC: 1874 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.34
DANN	Benign	0.38
PhyloP100		-0.93

Splicing

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

Other links and lift over

dbSNP: rs985492; hg19: chr18-29311034;