ENST00000415417.6:n.720T>A

Variant names:

• chr10-118365003-T-A
• rs1048828
• ENST00000415417.6:n.720T>A

Variant summary

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

The ENST00000415417.6(LINC00867):​n.720T>A 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 0.427 in 152,094 control chromosomes in the GnomAD database, including 15,688 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 0.43 (15686 hom., cov: 32)
  • Exomes 𝑓: 0.43 (2 hom.)
• Consequence: LINC00867 ENST00000415417.6 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.189
• Publications: 0 publications found

Genes affected

LINC00867 (HGNC:45265): (long intergenic non-protein coding RNA 867)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.532 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000415417.6. 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
	LINC00867	ENST00000415417.6	TSL:3	n.720T>A		non_coding_transcript_exon	Exon 4 of 4
	LINC00867	ENST00000453236.3	TSL:3	n.961T>A		non_coding_transcript_exon	Exon 3 of 3
	LINC00867	ENST00000657224.1		n.707T>A		non_coding_transcript_exon	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.428 AC: 65020 AN: 151960 Hom.: 15697 Cov.: 32

Gnomad AFR AF: 0.194

Gnomad AMI AF: 0.461

Gnomad AMR AF: 0.366

Gnomad ASJ AF: 0.503

Gnomad EAS AF: 0.480

Gnomad SAS AF: 0.525

Gnomad FIN AF: 0.639

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.536

Gnomad OTH AF: 0.423

GnomAD4 exome AF: 0.429 AC: 6 AN: 14 Hom.: 2 Cov.: 0 AF XY: 0.417 AC XY: 5 AN XY: 12

African (AFR) AC: 0 AN: 0

American (AMR) AF: 0.00 AC: 0 AN: 2

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AF: 0.500 AC: 1 AN: 2

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.500 AC: 5 AN: 10

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.427 AC: 65010 AN: 152080 Hom.: 15686 Cov.: 32 AF XY: 0.433 AC XY: 32213 AN XY: 74330

African (AFR) AF: 0.194 AC: 8054 AN: 41516

American (AMR) AF: 0.365 AC: 5577 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.503 AC: 1743 AN: 3466

East Asian (EAS) AF: 0.480 AC: 2480 AN: 5166

South Asian (SAS) AF: 0.525 AC: 2532 AN: 4824

European-Finnish (FIN) AF: 0.639 AC: 6754 AN: 10570

Middle Eastern (MID) AF: 0.398 AC: 117 AN: 294

European-Non Finnish (NFE) AF: 0.536 AC: 36451 AN: 67956

Other (OTH) AF: 0.418 AC: 882 AN: 2110

Alfa AF: 0.483 Hom.: 2353

Bravo AF: 0.392

Asia WGS AF: 0.430 AC: 1496 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	11
DANN	Benign	0.65
PhyloP100		0.19

Splicing

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

Other links and lift over

dbSNP: rs1048828; hg19: chr10-120124515;