chr13-60209335-T-C

Variant names:

• chr13-60209335-T-C
• rs78630578
• ENST00000755621.1:n.464+3229A>G

Variant summary

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

The ENST00000755621.1(LINC00434):​n.464+3229A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.672 in 152,068 control chromosomes in the GnomAD database, including 34,631 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 0.67 (34631 hom., cov: 33)
• Consequence: LINC00434 ENST00000755621.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.61
• Publications: 0 publications found

Genes affected

LINC00434 (HGNC:42769): (long intergenic non-protein coding RNA 434)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.11).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.757 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
LINC00434	ENST00000755621.1	n.464+3229A>G		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.672 AC: 102179 AN: 151950 Hom.: 34603 Cov.: 33

Gnomad AFR AF: 0.615

Gnomad AMI AF: 0.576

Gnomad AMR AF: 0.768

Gnomad ASJ AF: 0.677

Gnomad EAS AF: 0.540

Gnomad SAS AF: 0.631

Gnomad FIN AF: 0.637

Gnomad MID AF: 0.684

Gnomad NFE AF: 0.705

Gnomad OTH AF: 0.684

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

GnomAD4 genome AF: 0.672 AC: 102258 AN: 152068 Hom.: 34631 Cov.: 33 AF XY: 0.670 AC XY: 49787 AN XY: 74326

African (AFR) AF: 0.615 AC: 25525 AN: 41510

American (AMR) AF: 0.768 AC: 11747 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.677 AC: 2349 AN: 3470

East Asian (EAS) AF: 0.540 AC: 2799 AN: 5180

South Asian (SAS) AF: 0.632 AC: 3049 AN: 4828

European-Finnish (FIN) AF: 0.637 AC: 6689 AN: 10498

Middle Eastern (MID) AF: 0.684 AC: 201 AN: 294

European-Non Finnish (NFE) AF: 0.705 AC: 47933 AN: 67976

Other (OTH) AF: 0.682 AC: 1441 AN: 2112

Alfa AF: 0.692 Hom.: 38683

Bravo AF: 0.678

Asia WGS AF: 0.589 AC: 2051 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.12
DANN	Benign	0.20
PhyloP100		-2.6

Splicing

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

Other links and lift over

dbSNP: rs78630578; hg19: chr13-60783469; COSMIC: COSV69355525;