ENST00000843312.1:n.60T>G

Variant names:

• chr4-176651094-A-C
• rs12498670
• ENST00000843312.1:n.60T>G

Variant summary

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

The ENST00000843312.1(ENSG00000309713):​n.60T>G 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 0.492 in 152,122 control chromosomes in the GnomAD database, including 22,449 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 0.49 (22449 hom., cov: 33)
• Consequence: ENSG00000309713 ENST00000843312.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.48
• Publications: 2 publications found

Genes affected

ENSG00000309713 (HGNC:):

HAFML (HGNC:56694): (HuR (ELAVL1) associated fibroblast migratory lncRNA)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.65 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
ENSG00000309713	ENST00000843312.1	n.60T>G		non_coding_transcript_exon_variant	Exon 2 of 2
HAFML	ENST00000509194.2	n.67-18527A>C		intron_variant	Intron 1 of 2	3
ENSG00000309713	ENST00000843305.1	n.311-4361T>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.492 AC: 74840 AN: 152004 Hom.: 22444 Cov.: 33

Gnomad AFR AF: 0.135

Gnomad AMI AF: 0.695

Gnomad AMR AF: 0.580

Gnomad ASJ AF: 0.549

Gnomad EAS AF: 0.393

Gnomad SAS AF: 0.556

Gnomad FIN AF: 0.706

Gnomad MID AF: 0.415

Gnomad NFE AF: 0.655

Gnomad OTH AF: 0.504

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

GnomAD4 genome AF: 0.492 AC: 74855 AN: 152122 Hom.: 22449 Cov.: 33 AF XY: 0.495 AC XY: 36821 AN XY: 74344

African (AFR) AF: 0.135 AC: 5594 AN: 41534

American (AMR) AF: 0.580 AC: 8863 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.549 AC: 1904 AN: 3470

East Asian (EAS) AF: 0.393 AC: 2030 AN: 5170

South Asian (SAS) AF: 0.556 AC: 2670 AN: 4798

European-Finnish (FIN) AF: 0.706 AC: 7463 AN: 10572

Middle Eastern (MID) AF: 0.422 AC: 124 AN: 294

European-Non Finnish (NFE) AF: 0.655 AC: 44503 AN: 67980

Other (OTH) AF: 0.507 AC: 1070 AN: 2110

Alfa AF: 0.615 Hom.: 15171

Bravo AF: 0.466

Asia WGS AF: 0.491 AC: 1707 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	6.7
DANN	Benign	0.72
PhyloP100		1.5

Splicing

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

Other links and lift over

dbSNP: rs12498670; hg19: chr4-177572245;