chr1-209432291-TAGCAGCAGCAGC-T

Position:

• chr1-209432291-TAGCAGCAGCAGC-T

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The ENST00000433108.1(MIR205HG):​n.3123_3134delGCAGCAGCAGCA 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 0.618 in 1,332,644 control chromosomes in the GnomAD database, including 259,280 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.53 (24311 hom., cov: 0)
  • Exomes 𝑓: 0.63 (234969 hom.)
• Consequence: MIR205HG ENST00000433108.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.825

Genes affected

MIR205HG (HGNC:):

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.719 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MIR205HG	NR_145433.1	n.614_625delGCAGCAGCAGCA		non_coding_transcript_exon_variant	3/3
MIR205HG	NR_145434.1	n.749_760delGCAGCAGCAGCA		non_coding_transcript_exon_variant	5/5
MIR205HG	NR_145435.1	n.697_708delGCAGCAGCAGCA		non_coding_transcript_exon_variant	4/4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MIR205HG	ENST00000366437.7	n.475_486delGCAGCAGCAGCA		non_coding_transcript_exon_variant	4/4	3
MIR205HG	ENST00000429156.6	n.776_787delGCAGCAGCAGCA		non_coding_transcript_exon_variant	5/5	3
MIR205HG	ENST00000431096.6	n.697_708delGCAGCAGCAGCA		non_coding_transcript_exon_variant	4/4	3

Frequencies

GnomAD3 genomes AF: 0.534 AC: 79665 AN: 149280 Hom.: 24300 Cov.: 0

Gnomad AFR AF: 0.203

Gnomad AMI AF: 0.809

Gnomad AMR AF: 0.652

Gnomad ASJ AF: 0.685

Gnomad EAS AF: 0.739

Gnomad SAS AF: 0.647

Gnomad FIN AF: 0.643

Gnomad MID AF: 0.621

Gnomad NFE AF: 0.652

Gnomad OTH AF: 0.554

GnomAD3 exomes AF: 0.602 AC: 117179 AN: 194576 Hom.: 36454 AF XY: 0.605 AC XY: 63842 AN XY: 105446

Gnomad AFR exome AF: 0.177

Gnomad AMR exome AF: 0.668

Gnomad ASJ exome AF: 0.675

Gnomad EAS exome AF: 0.706

Gnomad SAS exome AF: 0.613

Gnomad FIN exome AF: 0.605

Gnomad NFE exome AF: 0.605

Gnomad OTH exome AF: 0.604

GnomAD4 exome AF: 0.629 AC: 744513 AN: 1183254 Hom.: 234969 AF XY: 0.628 AC XY: 367623 AN XY: 584962

Gnomad4 AFR exome AF: 0.166

Gnomad4 AMR exome AF: 0.660

Gnomad4 ASJ exome AF: 0.676

Gnomad4 EAS exome AF: 0.701

Gnomad4 SAS exome AF: 0.619

Gnomad4 FIN exome AF: 0.595

Gnomad4 NFE exome AF: 0.642

Gnomad4 OTH exome AF: 0.609

GnomAD4 genome AF: 0.533 AC: 79696 AN: 149390 Hom.: 24311 Cov.: 0 AF XY: 0.540 AC XY: 39331 AN XY: 72858

Gnomad4 AFR AF: 0.203

Gnomad4 AMR AF: 0.652

Gnomad4 ASJ AF: 0.685

Gnomad4 EAS AF: 0.739

Gnomad4 SAS AF: 0.649

Gnomad4 FIN AF: 0.643

Gnomad4 NFE AF: 0.652

Gnomad4 OTH AF: 0.559

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3842530; hg19: chr1-209605636;