6-135259815-T-C

Variant names:

• chr6-135259815-T-C
• rs2327587
• ENST00000791085.1:n.139-183T>C

Variant summary

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

The ENST00000791085.1(ENSG00000224374):​n.139-183T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.637 in 152,128 control chromosomes in the GnomAD database, including 33,177 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 0.64 (33177 hom., cov: 33)
• Consequence: ENSG00000224374 ENST00000791085.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.987
• Publications: 4 publications found

Genes affected

ENSG00000224374 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.895 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000791085.1. 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
	ENSG00000224374	ENST00000791085.1		n.139-183T>C		intron	N/A
	ENSG00000224374	ENST00000791086.1		n.196-183T>C		intron	N/A
	ENSG00000224374	ENST00000434255.1	TSL:5	n.-181T>C		upstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.636 AC: 96746 AN: 152010 Hom.: 33114 Cov.: 33

Gnomad AFR AF: 0.903

Gnomad AMI AF: 0.244

Gnomad AMR AF: 0.506

Gnomad ASJ AF: 0.465

Gnomad EAS AF: 0.435

Gnomad SAS AF: 0.509

Gnomad FIN AF: 0.601

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.550

Gnomad OTH AF: 0.575

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

GnomAD4 genome AF: 0.637 AC: 96874 AN: 152128 Hom.: 33177 Cov.: 33 AF XY: 0.635 AC XY: 47185 AN XY: 74338

African (AFR) AF: 0.903 AC: 37509 AN: 41532

American (AMR) AF: 0.507 AC: 7742 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.465 AC: 1612 AN: 3466

East Asian (EAS) AF: 0.434 AC: 2246 AN: 5174

South Asian (SAS) AF: 0.509 AC: 2450 AN: 4816

European-Finnish (FIN) AF: 0.601 AC: 6344 AN: 10552

Middle Eastern (MID) AF: 0.449 AC: 132 AN: 294

European-Non Finnish (NFE) AF: 0.550 AC: 37395 AN: 67996

Other (OTH) AF: 0.580 AC: 1222 AN: 2108

Alfa AF: 0.563 Hom.: 21326

Bravo AF: 0.638

Asia WGS AF: 0.529 AC: 1837 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.37
DANN	Benign	0.42
PhyloP100		-0.99

Splicing

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

Other links and lift over

dbSNP: rs2327587; hg19: chr6-135580953;