chr20-60502590-T-C

Position:

• chr20-60502590-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000659856.1(MIR646HG):​n.354-24797T>C variant causes a intron, non coding transcript 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 ENST00000659856.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00300

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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 male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 135 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MIR646HG	ENST00000659856.1	n.354-24797T>C		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.00922

Gnomad4 AMR AF: 0.0508

Gnomad4 ASJ AF: 0.0750

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00539

Gnomad4 FIN AF: 0.0132

Gnomad4 NFE AF: 0.0482

Gnomad4 OTH AF: 0.0426

Alfa AF: 0.0424 Hom.: 59

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17729098; hg19: chr20-59077648;