18-49634583-G-T

Variant names:

• chr18-49634583-G-T
• rs7241918
• ENST00000849192.1:n.231+21491G>T

Variant summary

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

The ENST00000849192.1(ENSG00000310339):​n.231+21491G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.88 in 152,220 control chromosomes in the GnomAD database, including 59,142 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 0.88 (59142 hom., cov: 33)
• Consequence: ENSG00000310339 ENST00000849192.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.485
• Publications: 82 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=-1.04).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.948 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.231+21491G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.880 AC: 133793 AN: 152102 Hom.: 59085 Cov.: 33

Gnomad AFR AF: 0.956

Gnomad AMI AF: 0.863

Gnomad AMR AF: 0.912

Gnomad ASJ AF: 0.903

Gnomad EAS AF: 0.873

Gnomad SAS AF: 0.867

Gnomad FIN AF: 0.839

Gnomad MID AF: 0.886

Gnomad NFE AF: 0.833

Gnomad OTH AF: 0.880

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

GnomAD4 genome AF: 0.880 AC: 133910 AN: 152220 Hom.: 59142 Cov.: 33 AF XY: 0.882 AC XY: 65613 AN XY: 74428

African (AFR) AF: 0.956 AC: 39723 AN: 41560

American (AMR) AF: 0.912 AC: 13951 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.903 AC: 3135 AN: 3470

East Asian (EAS) AF: 0.873 AC: 4526 AN: 5182

South Asian (SAS) AF: 0.868 AC: 4185 AN: 4824

European-Finnish (FIN) AF: 0.839 AC: 8859 AN: 10562

Middle Eastern (MID) AF: 0.891 AC: 262 AN: 294

European-Non Finnish (NFE) AF: 0.833 AC: 56621 AN: 68004

Other (OTH) AF: 0.882 AC: 1864 AN: 2114

Alfa AF: 0.853 Hom.: 228507

Bravo AF: 0.889

Asia WGS AF: 0.890 AC: 3093 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.3
DANN	Benign	0.22
PhyloP100		-0.48

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs7241918;

hg19: chr18-47160953;

COSMIC: COSV69621490;