ENST00000434512.1:n.184-327T>C

Variant names:

• chr13-51549383-T-C
• rs6650382
• ENST00000434512.1:n.184-327T>C

Variant summary

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

The ENST00000434512.1(INTS6-AS1):​n.184-327T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0666 in 152,142 control chromosomes in the GnomAD database, including 372 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 0.067 (372 hom., cov: 32)
• Consequence: INTS6-AS1 ENST00000434512.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.128
• Publications: 1 publications found

Genes affected

INTS6-AS1 (HGNC:42691): (INTS6 antisense RNA 1)

LOC124903175 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0832 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000434512.1. 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
	INTS6-AS1	ENST00000434512.1	TSL:3	n.184-327T>C		intron	N/A
	INTS6-AS1	ENST00000593672.5	TSL:5	n.520-327T>C		intron	N/A
	INTS6-AS1	ENST00000594959.5	TSL:5	n.664-327T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0666 AC: 10126 AN: 152024 Hom.: 371 Cov.: 32

Gnomad AFR AF: 0.0855

Gnomad AMI AF: 0.0603

Gnomad AMR AF: 0.0490

Gnomad ASJ AF: 0.0810

Gnomad EAS AF: 0.000577

Gnomad SAS AF: 0.0127

Gnomad FIN AF: 0.0786

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.0655

Gnomad OTH AF: 0.0599

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

GnomAD4 genome AF: 0.0666 AC: 10136 AN: 152142 Hom.: 372 Cov.: 32 AF XY: 0.0663 AC XY: 4934 AN XY: 74384

African (AFR) AF: 0.0855 AC: 3548 AN: 41490

American (AMR) AF: 0.0488 AC: 746 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0810 AC: 281 AN: 3468

East Asian (EAS) AF: 0.000578 AC: 3 AN: 5186

South Asian (SAS) AF: 0.0125 AC: 60 AN: 4818

European-Finnish (FIN) AF: 0.0786 AC: 833 AN: 10600

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.0656 AC: 4456 AN: 67974

Other (OTH) AF: 0.0597 AC: 126 AN: 2110

Alfa AF: 0.0637 Hom.: 177

Bravo AF: 0.0660

Asia WGS AF: 0.0120 AC: 42 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.1
DANN	Benign	0.64
PhyloP100		-0.13

Splicing

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

Other links and lift over

dbSNP: rs6650382; hg19: chr13-52123519;