chr18-75109329-C-T

Variant names:

• chr18-75109329-C-T
• rs17263755
• ENST00000744279.1:n.268+163G>A

Variant summary

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

The ENST00000744279.1(ENSG00000278911):​n.268+163G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.04 in 152,208 control chromosomes in the GnomAD database, including 170 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 0.040 (170 hom., cov: 33)
• Consequence: ENSG00000278911 ENST00000744279.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.19
• Publications: 1 publications found

Genes affected

ENSG00000278911 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0725 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000744279.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000278911	ENST00000744279.1		n.268+163G>A		intron	N/A
	ENSG00000278911	ENST00000744280.1		n.278+163G>A		intron	N/A
	ENSG00000278911	ENST00000744281.1		n.562+163G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0400 AC: 6082 AN: 152090 Hom.: 169 Cov.: 33

Gnomad AFR AF: 0.00963

Gnomad AMI AF: 0.0297

Gnomad AMR AF: 0.0760

Gnomad ASJ AF: 0.0254

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.0159

Gnomad FIN AF: 0.0386

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.0562

Gnomad OTH AF: 0.0455

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

GnomAD4 genome AF: 0.0400 AC: 6084 AN: 152208 Hom.: 170 Cov.: 33 AF XY: 0.0399 AC XY: 2967 AN XY: 74406

African (AFR) AF: 0.00961 AC: 399 AN: 41536

American (AMR) AF: 0.0761 AC: 1163 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0254 AC: 88 AN: 3468

East Asian (EAS) AF: 0.000194 AC: 1 AN: 5164

South Asian (SAS) AF: 0.0160 AC: 77 AN: 4824

European-Finnish (FIN) AF: 0.0386 AC: 409 AN: 10604

Middle Eastern (MID) AF: 0.0102 AC: 3 AN: 294

European-Non Finnish (NFE) AF: 0.0562 AC: 3822 AN: 68016

Other (OTH) AF: 0.0450 AC: 95 AN: 2112

Alfa AF: 0.0533 Hom.: 304

Bravo AF: 0.0423

Asia WGS AF: 0.0100 AC: 36 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.010
DANN	Benign	0.49
PhyloP100		-2.2

Splicing

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

Other links and lift over

dbSNP: rs17263755; hg19: chr18-72821285;