rs3087692

Variant names:

• chr19-4785315-G-A
• rs3087692
• ENST00000598782.3:n.570C>T

Your query was ambiguous. Multiple possible variants found:

• chr19-4785315-G-A
• chr19-4785315-G-T

Variant summary

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

The ENST00000766955.1(ENSG00000268536):​n.184C>T 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 0.17 in 152,206 control chromosomes in the GnomAD database, including 2,342 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 0.17 (2341 hom., cov: 32)
  • Exomes 𝑓: 0.051 (1 hom.)
• Consequence: ENSG00000268536 ENST00000766955.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.85
• Publications: 11 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=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.203 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.570C>T		non_coding_transcript_exon	Exon 2 of 2
	ENSG00000268536	ENST00000766955.1		n.184C>T		non_coding_transcript_exon	Exon 1 of 3
	ENSG00000268536	ENST00000766951.1		n.174+134C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.170 AC: 25802 AN: 152012 Hom.: 2337 Cov.: 32

Gnomad AFR AF: 0.206

Gnomad AMI AF: 0.161

Gnomad AMR AF: 0.128

Gnomad ASJ AF: 0.130

Gnomad EAS AF: 0.0388

Gnomad SAS AF: 0.0493

Gnomad FIN AF: 0.200

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.173

Gnomad OTH AF: 0.163

GnomAD4 exome AF: 0.0513 AC: 4 AN: 78 Hom.: 1 Cov.: 0 AF XY: 0.0741 AC XY: 4 AN XY: 54

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.00 AC: 0 AN: 2

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 6

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.0588 AC: 4 AN: 68

Other (OTH) AF: 0.00 AC: 0 AN: 2

GnomAD4 genome AF: 0.170 AC: 25824 AN: 152128 Hom.: 2341 Cov.: 32 AF XY: 0.168 AC XY: 12495 AN XY: 74368

African (AFR) AF: 0.206 AC: 8566 AN: 41504

American (AMR) AF: 0.128 AC: 1951 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.130 AC: 450 AN: 3466

East Asian (EAS) AF: 0.0389 AC: 201 AN: 5168

South Asian (SAS) AF: 0.0500 AC: 241 AN: 4824

European-Finnish (FIN) AF: 0.200 AC: 2119 AN: 10592

Middle Eastern (MID) AF: 0.163 AC: 48 AN: 294

European-Non Finnish (NFE) AF: 0.173 AC: 11761 AN: 67970

Other (OTH) AF: 0.161 AC: 340 AN: 2112

Alfa AF: 0.167 Hom.: 3549

Bravo AF: 0.164

Asia WGS AF: 0.0460 AC: 161 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	6.8
DANN	Benign	0.90
PhyloP100		1.8

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: rs3087692;

hg19: chr19-4785327;