5-159491886-G-A

Variant names:

• chr5-159491886-G-A
• rs10866713
• ENST00000636261.1:n.368-65618G>A

Variant summary

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

The ENST00000636261.1(ENSG00000249738):​n.368-65618G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.162 in 152,208 control chromosomes in the GnomAD database, including 2,136 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 0.16 (2136 hom., cov: 32)
• Consequence: ENSG00000249738 ENST00000636261.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.215
• Publications: 12 publications found

Genes affected

ENSG00000249738 (HGNC:58156):

ENSG00000283413 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.193 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000636261.1. 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
	ENSG00000249738	ENST00000636261.1	TSL:4	n.368-65618G>A		intron	N/A
	ENSG00000283413	ENST00000637629.2	TSL:5	n.184-3593C>T		intron	N/A
	ENSG00000249738	ENST00000764991.1		n.203-24026G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.162 AC: 24623 AN: 152090 Hom.: 2136 Cov.: 32

Gnomad AFR AF: 0.145

Gnomad AMI AF: 0.0471

Gnomad AMR AF: 0.142

Gnomad ASJ AF: 0.220

Gnomad EAS AF: 0.00192

Gnomad SAS AF: 0.143

Gnomad FIN AF: 0.120

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.195

Gnomad OTH AF: 0.165

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

GnomAD4 genome AF: 0.162 AC: 24625 AN: 152208 Hom.: 2136 Cov.: 32 AF XY: 0.155 AC XY: 11548 AN XY: 74426

African (AFR) AF: 0.145 AC: 6019 AN: 41542

American (AMR) AF: 0.142 AC: 2162 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.220 AC: 762 AN: 3470

East Asian (EAS) AF: 0.00193 AC: 10 AN: 5190

South Asian (SAS) AF: 0.143 AC: 690 AN: 4818

European-Finnish (FIN) AF: 0.120 AC: 1271 AN: 10606

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.195 AC: 13286 AN: 67988

Other (OTH) AF: 0.163 AC: 344 AN: 2112

Alfa AF: 0.184 Hom.: 1748

Bravo AF: 0.164

Asia WGS AF: 0.0660 AC: 230 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.83
DANN	Benign	0.42
PhyloP100		-0.21

Splicing

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

Other links and lift over

dbSNP: rs10866713; hg19: chr5-158918894;