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 ENST00000598782.3(ENSG00000268536):​n.570C>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 ENST00000598782.3 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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124904620	XR_007067103.1	n.308C>T		non_coding_transcript_exon_variant	Exon 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000268536	ENST00000598782.3	n.570C>T		non_coding_transcript_exon_variant	Exon 2 of 2	5
ENSG00000268536	ENST00000766955.1	n.184C>T		non_coding_transcript_exon_variant	Exon 1 of 3
ENSG00000268536	ENST00000766951.1	n.174+134C>T		intron_variant	Intron 2 of 4

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 v4.3

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

Other links and lift over

dbSNP: rs3087692; hg19: chr19-4785327;