ENST00000661392.1:n.348+32209C>T

Variant names:

• chr5-130766330-G-A
• rs1862647
• ENST00000661392.1:n.348+32209C>T

Variant summary

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

The ENST00000661392.1(ENSG00000287390):​n.348+32209C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.338 in 151,848 control chromosomes in the GnomAD database, including 8,870 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 0.34 (8870 hom., cov: 31)
• Consequence: ENSG00000287390 ENST00000661392.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.157
• Publications: 4 publications found

Genes affected

ENSG00000287390 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.42 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000661392.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000287390	ENST00000661392.1		n.348+32209C>T		intron	N/A
	ENSG00000287390	ENST00000804525.1		n.450+32209C>T		intron	N/A
	ENSG00000287390	ENST00000804527.1		n.469+32209C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.338 AC: 51225 AN: 151730 Hom.: 8843 Cov.: 31

Gnomad AFR AF: 0.358

Gnomad AMI AF: 0.0998

Gnomad AMR AF: 0.394

Gnomad ASJ AF: 0.318

Gnomad EAS AF: 0.435

Gnomad SAS AF: 0.393

Gnomad FIN AF: 0.362

Gnomad MID AF: 0.334

Gnomad NFE AF: 0.302

Gnomad OTH AF: 0.331

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

GnomAD4 genome AF: 0.338 AC: 51304 AN: 151848 Hom.: 8870 Cov.: 31 AF XY: 0.344 AC XY: 25502 AN XY: 74176

African (AFR) AF: 0.359 AC: 14855 AN: 41412

American (AMR) AF: 0.394 AC: 6023 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.318 AC: 1102 AN: 3468

East Asian (EAS) AF: 0.435 AC: 2244 AN: 5158

South Asian (SAS) AF: 0.394 AC: 1894 AN: 4808

European-Finnish (FIN) AF: 0.362 AC: 3812 AN: 10516

Middle Eastern (MID) AF: 0.332 AC: 97 AN: 292

European-Non Finnish (NFE) AF: 0.302 AC: 20484 AN: 67906

Other (OTH) AF: 0.333 AC: 702 AN: 2108

Alfa AF: 0.305 Hom.: 14115

Bravo AF: 0.339

Asia WGS AF: 0.452 AC: 1575 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.77
DANN	Benign	0.45
PhyloP100		-0.16

Splicing

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

Other links and lift over

dbSNP: rs1862647; hg19: chr5-130102023;