18-49708823-T-C

Variant names:

• chr18-49708823-T-C
• rs1943985
• ENST00000849189.1:n.712+8466T>C

Variant summary

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

The ENST00000849189.1(ENSG00000310339):​n.712+8466T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.157 in 151,956 control chromosomes in the GnomAD database, including 1,920 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 0.16 (1920 hom., cov: 32)
• Consequence: ENSG00000310339 ENST00000849189.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.30
• Publications: 2 publications found

Genes affected

ENSG00000310339 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.179 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105372112	XR_007066363.1	n.642+8466T>C		intron_variant	Intron 3 of 4
LOC105372112	XR_007066364.1	n.887+8466T>C		intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000310339	ENST00000849189.1	n.712+8466T>C		intron_variant	Intron 3 of 3
ENSG00000310339	ENST00000849190.1	n.404+8466T>C		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.157 AC: 23872 AN: 151838 Hom.: 1917 Cov.: 32

Gnomad AFR AF: 0.182

Gnomad AMI AF: 0.0987

Gnomad AMR AF: 0.168

Gnomad ASJ AF: 0.0986

Gnomad EAS AF: 0.144

Gnomad SAS AF: 0.184

Gnomad FIN AF: 0.126

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.147

Gnomad OTH AF: 0.156

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

GnomAD4 genome AF: 0.157 AC: 23893 AN: 151956 Hom.: 1920 Cov.: 32 AF XY: 0.158 AC XY: 11762 AN XY: 74270

African (AFR) AF: 0.182 AC: 7553 AN: 41422

American (AMR) AF: 0.168 AC: 2570 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.0986 AC: 342 AN: 3468

East Asian (EAS) AF: 0.144 AC: 743 AN: 5158

South Asian (SAS) AF: 0.184 AC: 882 AN: 4786

European-Finnish (FIN) AF: 0.126 AC: 1333 AN: 10574

Middle Eastern (MID) AF: 0.163 AC: 48 AN: 294

European-Non Finnish (NFE) AF: 0.147 AC: 10008 AN: 67964

Other (OTH) AF: 0.154 AC: 324 AN: 2106

Alfa AF: 0.108 Hom.: 210

Bravo AF: 0.162

Asia WGS AF: 0.161 AC: 557 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.015
DANN	Benign	0.34
PhyloP100		-3.3

Splicing

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

Other links and lift over

dbSNP: rs1943985; hg19: chr18-47235193;