chr18-49640844-T-C

Variant names:

• chr18-49640844-T-C
• rs4939883
• ENST00000849192.1:n.232-16043T>C

Variant summary

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

The ENST00000849192.1(ENSG00000310339):​n.232-16043T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.754 in 152,102 control chromosomes in the GnomAD database, including 44,641 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 0.75 (44641 hom., cov: 32)
• Consequence: ENSG00000310339 ENST00000849192.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.398
• Publications: 98 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=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.841 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000849192.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000310339	ENST00000849192.1		n.232-16043T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.754 AC: 114612 AN: 151984 Hom.: 44618 Cov.: 32

Gnomad AFR AF: 0.541

Gnomad AMI AF: 0.860

Gnomad AMR AF: 0.853

Gnomad ASJ AF: 0.894

Gnomad EAS AF: 0.806

Gnomad SAS AF: 0.861

Gnomad FIN AF: 0.836

Gnomad MID AF: 0.813

Gnomad NFE AF: 0.827

Gnomad OTH AF: 0.777

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

GnomAD4 genome AF: 0.754 AC: 114675 AN: 152102 Hom.: 44641 Cov.: 32 AF XY: 0.760 AC XY: 56508 AN XY: 74378

African (AFR) AF: 0.541 AC: 22415 AN: 41438

American (AMR) AF: 0.853 AC: 13046 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.894 AC: 3104 AN: 3472

East Asian (EAS) AF: 0.806 AC: 4161 AN: 5160

South Asian (SAS) AF: 0.862 AC: 4162 AN: 4826

European-Finnish (FIN) AF: 0.836 AC: 8856 AN: 10596

Middle Eastern (MID) AF: 0.810 AC: 238 AN: 294

European-Non Finnish (NFE) AF: 0.827 AC: 56262 AN: 67996

Other (OTH) AF: 0.778 AC: 1647 AN: 2116

Alfa AF: 0.811 Hom.: 180396

Bravo AF: 0.747

Asia WGS AF: 0.833 AC: 2897 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.56
DANN	Benign	0.70
PhyloP100		0.40

Splicing

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

Other links and lift over

dbSNP: rs4939883; hg19: chr18-47167214;