19-54518184-G-C

Variant names:

• chr19-54518184-G-C
• rs4591276
• ENST00000849740.1:n.464-3040C>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000849740.1(ENSG00000310422):​n.464-3040C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.018 in 152,260 control chromosomes in the GnomAD database, including 28 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 0.018 (28 hom., cov: 32)
• Consequence: ENSG00000310422 ENST00000849740.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0170
• Publications: 1 publications found

Genes affected

ENSG00000310422 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BS1: Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.018 (2746/152260) while in subpopulation NFE AF = 0.0264 (1796/68016). AF 95% confidence interval is 0.0254. There are 28 homozygotes in GnomAd4. There are 1315 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 28 gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000849740.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000310422	ENST00000849740.1		n.464-3040C>G		intron	N/A
	ENSG00000310422	ENST00000849741.1		n.372-3040C>G		intron	N/A
	ENSG00000310422	ENST00000849742.1		n.308-1876C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0180 AC: 2745 AN: 152142 Hom.: 28 Cov.: 32

Gnomad AFR AF: 0.00497

Gnomad AMI AF: 0.0307

Gnomad AMR AF: 0.0102

Gnomad ASJ AF: 0.0432

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00663

Gnomad FIN AF: 0.0331

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0264

Gnomad OTH AF: 0.0134

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

GnomAD4 genome AF: 0.0180 AC: 2746 AN: 152260 Hom.: 28 Cov.: 32 AF XY: 0.0177 AC XY: 1315 AN XY: 74432

African (AFR) AF: 0.00496 AC: 206 AN: 41560

American (AMR) AF: 0.0101 AC: 155 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0432 AC: 150 AN: 3470

East Asian (EAS) AF: 0.00 AC: 0 AN: 5182

South Asian (SAS) AF: 0.00663 AC: 32 AN: 4824

European-Finnish (FIN) AF: 0.0331 AC: 351 AN: 10602

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.0264 AC: 1796 AN: 68016

Other (OTH) AF: 0.0133 AC: 28 AN: 2112

Alfa AF: 0.00982 Hom.: 1

Bravo AF: 0.0161

Asia WGS AF: 0.00318 AC: 11 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.4
DANN	Benign	0.64
PhyloP100		-0.017

Splicing

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

Other links and lift over

dbSNP: rs4591276; hg19: chr19-55029367;