rs12460989

Variant names:

• chr19-4785155-T-G
• rs12460989
• ENST00000598782.3:n.730A>C

Variant summary

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

The ENST00000766955.1(ENSG00000268536):​n.340+4A>C variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.111 in 151,846 control chromosomes in the GnomAD database, including 1,658 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 0.11 (1658 hom., cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000268536 ENST00000766955.1 splice_region, intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.56
• Publications: 3 publications found

Genes affected

ENSG00000268536 (HGNC:):

MIR7-3HG (HGNC:30049): (MIR7-3 host gene)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.06).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.262 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000766955.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000268536	ENST00000598782.3	TSL:5	n.730A>C		non_coding_transcript_exon	Exon 2 of 2
	ENSG00000268536	ENST00000766951.1		n.174+294A>C		intron	N/A
	ENSG00000268536	ENST00000766952.1		n.174+294A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.111 AC: 16839 AN: 151740 Hom.: 1643 Cov.: 32

Gnomad AFR AF: 0.266

Gnomad AMI AF: 0.0132

Gnomad AMR AF: 0.118

Gnomad ASJ AF: 0.0585

Gnomad EAS AF: 0.0506

Gnomad SAS AF: 0.0848

Gnomad FIN AF: 0.0372

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0381

Gnomad OTH AF: 0.0982

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 4 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 2

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

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

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 4

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.111 AC: 16904 AN: 151846 Hom.: 1658 Cov.: 32 AF XY: 0.110 AC XY: 8173 AN XY: 74210

African (AFR) AF: 0.266 AC: 11015 AN: 41388

American (AMR) AF: 0.118 AC: 1805 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.0585 AC: 203 AN: 3468

East Asian (EAS) AF: 0.0508 AC: 262 AN: 5162

South Asian (SAS) AF: 0.0841 AC: 404 AN: 4804

European-Finnish (FIN) AF: 0.0372 AC: 392 AN: 10536

Middle Eastern (MID) AF: 0.0374 AC: 11 AN: 294

European-Non Finnish (NFE) AF: 0.0381 AC: 2590 AN: 67926

Other (OTH) AF: 0.0995 AC: 210 AN: 2110

Alfa AF: 0.0808 Hom.: 131

Bravo AF: 0.121

Asia WGS AF: 0.112 AC: 388 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.22
DANN	Benign	0.20
PhyloP100		-2.6

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs12460989;

hg19: chr19-4785167;