chr13-51549383-T-C

Position:

• chr13-51549383-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000657609.1(INTS6-AS1):​n.91-327T>C variant causes a intron, non coding transcript 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 ENST00000657609.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.128

Genes affected

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

LOC124903175 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124903175	XR_007063804.1	n.107+153T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
INTS6-AS1	ENST00000657609.1	n.91-327T>C		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.0855

Gnomad4 AMR AF: 0.0488

Gnomad4 ASJ AF: 0.0810

Gnomad4 EAS AF: 0.000578

Gnomad4 SAS AF: 0.0125

Gnomad4 FIN AF: 0.0786

Gnomad4 NFE AF: 0.0656

Gnomad4 OTH AF: 0.0597

Alfa AF: 0.0627 Hom.: 155

Bravo AF: 0.0660

Asia WGS AF: 0.0120 AC: 42 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6650382; hg19: chr13-52123519;