rs6536413

Variant names:

• chr4-159361566-C-A
• rs6536413
• ENST00000837042.1:n.170+660C>A

Variant summary

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

The ENST00000837042.1(ENSG00000308878):​n.170+660C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.117 in 152,110 control chromosomes in the GnomAD database, including 1,126 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 0.12 (1126 hom., cov: 31)
• Consequence: ENSG00000308878 ENST00000837042.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.103
• Publications: 6 publications found

Genes affected

ENSG00000308878 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.185 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
ENSG00000308878	ENST00000837042.1	n.170+660C>A		intron_variant	Intron 1 of 1
ENSG00000308878	ENST00000837043.1	n.149+660C>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.117 AC: 17849 AN: 151992 Hom.: 1122 Cov.: 31

Gnomad AFR AF: 0.0992

Gnomad AMI AF: 0.166

Gnomad AMR AF: 0.190

Gnomad ASJ AF: 0.0930

Gnomad EAS AF: 0.0484

Gnomad SAS AF: 0.0963

Gnomad FIN AF: 0.0564

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.128

Gnomad OTH AF: 0.136

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

GnomAD4 genome AF: 0.117 AC: 17861 AN: 152110 Hom.: 1126 Cov.: 31 AF XY: 0.115 AC XY: 8562 AN XY: 74364

African (AFR) AF: 0.0990 AC: 4109 AN: 41486

American (AMR) AF: 0.190 AC: 2906 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.0930 AC: 323 AN: 3472

East Asian (EAS) AF: 0.0483 AC: 250 AN: 5174

South Asian (SAS) AF: 0.0966 AC: 465 AN: 4816

European-Finnish (FIN) AF: 0.0564 AC: 598 AN: 10596

Middle Eastern (MID) AF: 0.139 AC: 41 AN: 294

European-Non Finnish (NFE) AF: 0.128 AC: 8731 AN: 67980

Other (OTH) AF: 0.136 AC: 287 AN: 2112

Alfa AF: 0.125 Hom.: 2143

Bravo AF: 0.127

Asia WGS AF: 0.0960 AC: 333 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.0
DANN	Benign	0.69
PhyloP100		-0.10

Splicing

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

Other links and lift over

dbSNP: rs6536413; hg19: chr4-160282718;