chr5-131103398-T-C

Variant names:

• chr5-131103398-T-C
• rs3891636
• ENST00000840920.1:n.487-6393T>C

Variant summary

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

The ENST00000840920.1(ENSG00000309416):​n.487-6393T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.302 in 151,830 control chromosomes in the GnomAD database, including 8,198 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 0.30 (8198 hom., cov: 31)
• Consequence: ENSG00000309416 ENST00000840920.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.273
• Publications: 7 publications found

Genes affected

ENSG00000309416 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.5 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000840920.1. 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
	ENSG00000309416	ENST00000840920.1		n.487-6393T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.302 AC: 45783 AN: 151710 Hom.: 8178 Cov.: 31

Gnomad AFR AF: 0.505

Gnomad AMI AF: 0.0570

Gnomad AMR AF: 0.218

Gnomad ASJ AF: 0.195

Gnomad EAS AF: 0.216

Gnomad SAS AF: 0.267

Gnomad FIN AF: 0.268

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.221

Gnomad OTH AF: 0.274

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

GnomAD4 genome AF: 0.302 AC: 45836 AN: 151830 Hom.: 8198 Cov.: 31 AF XY: 0.300 AC XY: 22224 AN XY: 74190

African (AFR) AF: 0.505 AC: 20893 AN: 41344

American (AMR) AF: 0.217 AC: 3312 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.195 AC: 676 AN: 3464

East Asian (EAS) AF: 0.216 AC: 1109 AN: 5146

South Asian (SAS) AF: 0.268 AC: 1288 AN: 4812

European-Finnish (FIN) AF: 0.268 AC: 2823 AN: 10514

Middle Eastern (MID) AF: 0.255 AC: 75 AN: 294

European-Non Finnish (NFE) AF: 0.221 AC: 15029 AN: 67974

Other (OTH) AF: 0.274 AC: 579 AN: 2110

Alfa AF: 0.246 Hom.: 14411

Bravo AF: 0.301

Asia WGS AF: 0.292 AC: 1016 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	4.9
DANN	Benign	0.36
PhyloP100		0.27

Splicing

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

Other links and lift over

dbSNP: rs3891636; hg19: chr5-130439091;