rs17729098

Variant names:

• chr20-60502590-T-C
• rs17729098
• ENST00000437035.5:n.428-24797T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000437035.5(MIR646HG):​n.428-24797T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0328 in 152,272 control chromosomes in the GnomAD database, including 135 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 0.033 (135 hom., cov: 32)
• Consequence: MIR646HG ENST00000437035.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00300
• Publications: 2 publications found

Genes affected

MIR646HG (HGNC:27659): (MIR646 host gene)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BS1: Variant frequency is greater than expected in population amr. GnomAd4 allele frequency = 0.0328 (4996/152272) while in subpopulation AMR AF = 0.0508 (777/15298). AF 95% confidence interval is 0.0478. There are 135 homozygotes in GnomAd4. There are 2340 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 135 gene

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
MIR646HG	ENST00000437035.5	n.428-24797T>C		intron_variant	Intron 4 of 4	5
MIR646HG	ENST00000659856.1	n.354-24797T>C		intron_variant	Intron 3 of 5
MIR646HG	ENST00000665114.1	n.359-24797T>C		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes AF: 0.0328 AC: 4995 AN: 152154 Hom.: 135 Cov.: 32

Gnomad AFR AF: 0.00927

Gnomad AMI AF: 0.0406

Gnomad AMR AF: 0.0509

Gnomad ASJ AF: 0.0750

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00517

Gnomad FIN AF: 0.0132

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0481

Gnomad OTH AF: 0.0431

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

GnomAD4 genome AF: 0.0328 AC: 4996 AN: 152272 Hom.: 135 Cov.: 32 AF XY: 0.0314 AC XY: 2340 AN XY: 74454

African (AFR) AF: 0.00922 AC: 383 AN: 41552

American (AMR) AF: 0.0508 AC: 777 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0750 AC: 260 AN: 3468

East Asian (EAS) AF: 0.00 AC: 0 AN: 5172

South Asian (SAS) AF: 0.00539 AC: 26 AN: 4828

European-Finnish (FIN) AF: 0.0132 AC: 140 AN: 10622

Middle Eastern (MID) AF: 0.0238 AC: 7 AN: 294

European-Non Finnish (NFE) AF: 0.0482 AC: 3276 AN: 68014

Other (OTH) AF: 0.0426 AC: 90 AN: 2112

Alfa AF: 0.0450 Hom.: 101

Bravo AF: 0.0345

Asia WGS AF: 0.00433 AC: 15 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.3
DANN	Benign	0.66
PhyloP100		-0.0030
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs17729098; hg19: chr20-59077648;