ENST00000635333.1:n.327+7207C>A

Variant names:

• chr5-159399784-C-A
• rs6871626
• ENST00000635333.1:n.327+7207C>A

Variant summary

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

The ENST00000635333.1(ENSG00000249738):​n.327+7207C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.288 in 151,938 control chromosomes in the GnomAD database, including 6,570 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 0.29 (6570 hom., cov: 31)
• Consequence: ENSG00000249738 ENST00000635333.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.285
• Publications: 82 publications found

Genes affected

ENSG00000249738 (HGNC:58156):

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 (SAS) allele frequency at 95% confidence interval = 0.365 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000635333.1. 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
	ENSG00000249738	ENST00000635333.1	TSL:5	n.327+7207C>A		intron	N/A
	ENSG00000249738	ENST00000641150.1		n.533-16740C>A		intron	N/A
	ENSG00000249738	ENST00000648969.1		n.54-16740C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.288 AC: 43724 AN: 151820 Hom.: 6566 Cov.: 31

Gnomad AFR AF: 0.191

Gnomad AMI AF: 0.348

Gnomad AMR AF: 0.274

Gnomad ASJ AF: 0.233

Gnomad EAS AF: 0.344

Gnomad SAS AF: 0.380

Gnomad FIN AF: 0.291

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.340

Gnomad OTH AF: 0.300

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

GnomAD4 genome AF: 0.288 AC: 43744 AN: 151938 Hom.: 6570 Cov.: 31 AF XY: 0.286 AC XY: 21259 AN XY: 74250

African (AFR) AF: 0.191 AC: 7929 AN: 41438

American (AMR) AF: 0.274 AC: 4185 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.233 AC: 806 AN: 3466

East Asian (EAS) AF: 0.345 AC: 1771 AN: 5140

South Asian (SAS) AF: 0.379 AC: 1825 AN: 4814

European-Finnish (FIN) AF: 0.291 AC: 3067 AN: 10542

Middle Eastern (MID) AF: 0.340 AC: 100 AN: 294

European-Non Finnish (NFE) AF: 0.340 AC: 23114 AN: 67950

Other (OTH) AF: 0.299 AC: 631 AN: 2108

Alfa AF: 0.323 Hom.: 24776

Bravo AF: 0.282

Asia WGS AF: 0.361 AC: 1255 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.0
DANN	Benign	0.49
PhyloP100		-0.28

Splicing

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

Other links and lift over

dbSNP: rs6871626; hg19: chr5-158826792;