19-5886517-C-G

Variant names:

• chr19-5886517-C-G
• rs1678869
• ENST00000585661.1:c.307+9936G>C

Variant summary

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

The ENST00000585661.1(ENSG00000267740):​c.307+9936G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.852 in 152,254 control chromosomes in the GnomAD database, including 55,405 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 0.85 (55405 hom., cov: 33)
• Consequence: ENSG00000267740 ENST00000585661.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.259
• Publications: 3 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 = 0.869 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000267740	ENST00000585661.1	c.307+9936G>C		intron_variant	Intron 3 of 3	2		ENSP00000467210.1
ENSG00000267740	ENST00000586349.5	c.382+9936G>C		intron_variant	Intron 3 of 3	2		ENSP00000466639.1
ENSG00000267740	ENST00000592091.5	n.313+9936G>C		intron_variant	Intron 3 of 4	2		ENSP00000465499.1

Frequencies

GnomAD3 genomes AF: 0.852 AC: 129663 AN: 152136 Hom.: 55360 Cov.: 33

Gnomad AFR AF: 0.842

Gnomad AMI AF: 0.844

Gnomad AMR AF: 0.881

Gnomad ASJ AF: 0.911

Gnomad EAS AF: 0.814

Gnomad SAS AF: 0.756

Gnomad FIN AF: 0.803

Gnomad MID AF: 0.867

Gnomad NFE AF: 0.866

Gnomad OTH AF: 0.859

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

GnomAD4 genome AF: 0.852 AC: 129762 AN: 152254 Hom.: 55405 Cov.: 33 AF XY: 0.850 AC XY: 63269 AN XY: 74448

African (AFR) AF: 0.842 AC: 34990 AN: 41552

American (AMR) AF: 0.881 AC: 13483 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.911 AC: 3163 AN: 3472

East Asian (EAS) AF: 0.814 AC: 4211 AN: 5174

South Asian (SAS) AF: 0.755 AC: 3646 AN: 4830

European-Finnish (FIN) AF: 0.803 AC: 8520 AN: 10604

Middle Eastern (MID) AF: 0.871 AC: 256 AN: 294

European-Non Finnish (NFE) AF: 0.866 AC: 58915 AN: 68010

Other (OTH) AF: 0.857 AC: 1812 AN: 2114

Alfa AF: 0.862 Hom.: 6996

Bravo AF: 0.860

Asia WGS AF: 0.765 AC: 2663 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.72
DANN	Benign	0.61
PhyloP100		-0.26
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: rs1678869; hg19: chr19-5886528;