rs6485438

Variant names:

• chr11-43665068-G-A
• rs6485438
• XM_024448571.2:c.-63+24034G>A

Variant summary

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

The ENST00000526615.6(MIR670HG):​n.287-7923G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.315 in 151,982 control chromosomes in the GnomAD database, including 7,768 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 0.32 (7768 hom., cov: 32)
• Consequence: MIR670HG ENST00000526615.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.453
• Publications: 8 publications found

Genes affected

HSD17B12 (HGNC:18646): (hydroxysteroid 17-beta dehydrogenase 12) This gene encodes a very important 17beta-hydroxysteroid dehydrogenase (17beta-HSD) that converts estrone into estradiol in ovarian tissue. This enzyme is also involved in fatty acid elongation. [provided by RefSeq, Oct 2011]

MIR670HG (HGNC:49204): (MIR670 host gene)

ENSG00000283341 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.355 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000526615.6. 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
	MIR670HG	ENST00000526615.6	TSL:3	n.287-7923G>A		intron	N/A
	ENSG00000283341	ENST00000529261.5	TSL:3	n.312-7923G>A		intron	N/A
	ENSG00000283341	ENST00000532864.6	TSL:5	n.281+24034G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.315 AC: 47894 AN: 151864 Hom.: 7761 Cov.: 32

Gnomad AFR AF: 0.360

Gnomad AMI AF: 0.310

Gnomad AMR AF: 0.267

Gnomad ASJ AF: 0.346

Gnomad EAS AF: 0.207

Gnomad SAS AF: 0.307

Gnomad FIN AF: 0.327

Gnomad MID AF: 0.331

Gnomad NFE AF: 0.305

Gnomad OTH AF: 0.316

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

GnomAD4 genome AF: 0.315 AC: 47914 AN: 151982 Hom.: 7768 Cov.: 32 AF XY: 0.313 AC XY: 23225 AN XY: 74294

African (AFR) AF: 0.360 AC: 14893 AN: 41424

American (AMR) AF: 0.266 AC: 4068 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.346 AC: 1200 AN: 3466

East Asian (EAS) AF: 0.208 AC: 1076 AN: 5180

South Asian (SAS) AF: 0.307 AC: 1481 AN: 4818

European-Finnish (FIN) AF: 0.327 AC: 3445 AN: 10548

Middle Eastern (MID) AF: 0.332 AC: 97 AN: 292

European-Non Finnish (NFE) AF: 0.305 AC: 20710 AN: 67964

Other (OTH) AF: 0.314 AC: 662 AN: 2110

Alfa AF: 0.313 Hom.: 8721

Bravo AF: 0.315

Asia WGS AF: 0.291 AC: 1014 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	2.9
DANN	Benign	0.55
PhyloP100		0.45

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: rs6485438;

hg19: chr11-43686618;