6-86756774-A-G

Variant names:

• chr6-86756774-A-G
• rs493187
• ENST00000782919.1:n.539T>C

Variant summary

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

The ENST00000782919.1(ENSG00000301924):​n.539T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.511 in 151,930 control chromosomes in the GnomAD database, including 20,799 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 0.51 (20799 hom., cov: 32)
• Consequence: ENSG00000301924 ENST00000782919.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.493
• Publications: 8 publications found

Genes affected

ENSG00000301924 (HGNC:):

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 (AFR) allele frequency at 95% confidence interval = 0.687 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000301924	ENST00000782919.1	n.539T>C		non_coding_transcript_exon_variant	Exon 5 of 5
ENSG00000301924	ENST00000782920.1	n.321T>C		non_coding_transcript_exon_variant	Exon 3 of 3
ENSG00000301924	ENST00000782921.1	n.294T>C		non_coding_transcript_exon_variant	Exon 4 of 4

Frequencies

GnomAD3 genomes AF: 0.510 AC: 77499 AN: 151812 Hom.: 20771 Cov.: 32

Gnomad AFR AF: 0.694

Gnomad AMI AF: 0.376

Gnomad AMR AF: 0.455

Gnomad ASJ AF: 0.505

Gnomad EAS AF: 0.505

Gnomad SAS AF: 0.438

Gnomad FIN AF: 0.396

Gnomad MID AF: 0.579

Gnomad NFE AF: 0.437

Gnomad OTH AF: 0.511

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

GnomAD4 genome AF: 0.511 AC: 77573 AN: 151930 Hom.: 20799 Cov.: 32 AF XY: 0.506 AC XY: 37586 AN XY: 74290

African (AFR) AF: 0.694 AC: 28750 AN: 41442

American (AMR) AF: 0.454 AC: 6934 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.505 AC: 1748 AN: 3462

East Asian (EAS) AF: 0.506 AC: 2609 AN: 5158

South Asian (SAS) AF: 0.438 AC: 2108 AN: 4808

European-Finnish (FIN) AF: 0.396 AC: 4169 AN: 10540

Middle Eastern (MID) AF: 0.578 AC: 170 AN: 294

European-Non Finnish (NFE) AF: 0.437 AC: 29657 AN: 67934

Other (OTH) AF: 0.514 AC: 1085 AN: 2110

Alfa AF: 0.458 Hom.: 74987

Bravo AF: 0.523

Asia WGS AF: 0.471 AC: 1636 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.2
DANN	Benign	0.61
PhyloP100		0.49

Splicing

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

Other links and lift over

dbSNP: rs493187; hg19: chr6-87466492; COSMIC: COSV69412041;