19-5886721-T-C

Variant names:

• chr19-5886721-T-C
• rs1674159
• ENST00000585661.1:c.307+9732A>G

Variant summary

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

The ENST00000585661.1(ENSG00000267740):​c.307+9732A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.86 in 152,178 control chromosomes in the GnomAD database, including 56,397 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 0.86 (56397 hom., cov: 32)
• Consequence: ENSG00000267740 ENST00000585661.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.580
• Publications: 16 publications found

Genes affected

ENSG00000267740 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.871 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000585661.1. 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
	ENSG00000267740	ENST00000585661.1	TSL:2	c.307+9732A>G		intron	N/A	ENSP00000467210.1	K7EP35
	ENSG00000267740	ENST00000586349.5	TSL:2	c.382+9732A>G		intron	N/A	ENSP00000466639.1	K7EMT4
	ENSG00000267740	ENST00000592091.5	TSL:2	n.313+9732A>G		intron	N/A	ENSP00000465499.1	K7EK78

Frequencies

GnomAD3 genomes AF: 0.860 AC: 130824 AN: 152060 Hom.: 56353 Cov.: 32

Gnomad AFR AF: 0.869

Gnomad AMI AF: 0.841

Gnomad AMR AF: 0.883

Gnomad ASJ AF: 0.912

Gnomad EAS AF: 0.814

Gnomad SAS AF: 0.759

Gnomad FIN AF: 0.804

Gnomad MID AF: 0.873

Gnomad NFE AF: 0.867

Gnomad OTH AF: 0.868

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

GnomAD4 genome AF: 0.860 AC: 130922 AN: 152178 Hom.: 56397 Cov.: 32 AF XY: 0.858 AC XY: 63841 AN XY: 74386

African (AFR) AF: 0.869 AC: 36098 AN: 41534

American (AMR) AF: 0.884 AC: 13519 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.912 AC: 3164 AN: 3470

East Asian (EAS) AF: 0.814 AC: 4193 AN: 5152

South Asian (SAS) AF: 0.758 AC: 3655 AN: 4822

European-Finnish (FIN) AF: 0.804 AC: 8517 AN: 10594

Middle Eastern (MID) AF: 0.878 AC: 258 AN: 294

European-Non Finnish (NFE) AF: 0.867 AC: 58925 AN: 67992

Other (OTH) AF: 0.866 AC: 1826 AN: 2108

Alfa AF: 0.868 Hom.: 163821

Bravo AF: 0.868

Asia WGS AF: 0.768 AC: 2674 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.79
DANN	Benign	0.43
PhyloP100		-0.58
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs1674159; hg19: chr19-5886732;