chr1-209431757-A-G

Variant names:

• chr1-209431757-A-G
• rs2249632
• ENST00000429156.7:n.594A>G

Variant summary

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

The ENST00000429156.7(MIR205HG):​n.594A>G 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 0.549 in 209,298 control chromosomes in the GnomAD database, including 35,374 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 0.53 (24728 hom., cov: 32)
  • Exomes 𝑓: 0.59 (10646 hom.)
• Consequence: MIR205HG ENST00000429156.7 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.368
• Publications: 7 publications found

Genes affected

MIR205HG (HGNC:43562): (MIR205 host gene)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.727 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MIR205HG	NR_145434.1	n.564A>G		non_coding_transcript_exon_variant	Exon 4 of 5
MIR205HG	NR_145435.1	n.512A>G		non_coding_transcript_exon_variant	Exon 3 of 4
MIR205HG	NR_145433.1	n.498-447A>G		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIR205HG	ENST00000429156.7	n.594A>G		non_coding_transcript_exon_variant	Exon 4 of 5	3
MIR205HG	ENST00000431096.7	n.515A>G		non_coding_transcript_exon_variant	Exon 3 of 4	3
MIR205HG	ENST00000433108.1	n.2938A>G		non_coding_transcript_exon_variant	Exon 1 of 2	2

Frequencies

GnomAD3 genomes AF: 0.532 AC: 80865 AN: 151996 Hom.: 24716 Cov.: 32

Gnomad AFR AF: 0.201

Gnomad AMI AF: 0.810

Gnomad AMR AF: 0.651

Gnomad ASJ AF: 0.686

Gnomad EAS AF: 0.747

Gnomad SAS AF: 0.652

Gnomad FIN AF: 0.645

Gnomad MID AF: 0.623

Gnomad NFE AF: 0.652

Gnomad OTH AF: 0.556

GnomAD4 exome AF: 0.594 AC: 33962 AN: 57182 Hom.: 10646 Cov.: 0 AF XY: 0.598 AC XY: 17633 AN XY: 29476

African (AFR) AF: 0.144 AC: 430 AN: 2994

American (AMR) AF: 0.656 AC: 2509 AN: 3822

Ashkenazi Jewish (ASJ) AF: 0.657 AC: 876 AN: 1334

East Asian (EAS) AF: 0.715 AC: 2706 AN: 3782

South Asian (SAS) AF: 0.600 AC: 3821 AN: 6370

European-Finnish (FIN) AF: 0.558 AC: 899 AN: 1612

Middle Eastern (MID) AF: 0.599 AC: 121 AN: 202

European-Non Finnish (NFE) AF: 0.612 AC: 20914 AN: 34186

Other (OTH) AF: 0.585 AC: 1686 AN: 2880

GnomAD4 genome AF: 0.532 AC: 80898 AN: 152116 Hom.: 24728 Cov.: 32 AF XY: 0.539 AC XY: 40053 AN XY: 74356

African (AFR) AF: 0.201 AC: 8332 AN: 41518

American (AMR) AF: 0.651 AC: 9961 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.686 AC: 2380 AN: 3470

East Asian (EAS) AF: 0.746 AC: 3853 AN: 5162

South Asian (SAS) AF: 0.653 AC: 3147 AN: 4816

European-Finnish (FIN) AF: 0.645 AC: 6833 AN: 10590

Middle Eastern (MID) AF: 0.633 AC: 186 AN: 294

European-Non Finnish (NFE) AF: 0.652 AC: 44287 AN: 67956

Other (OTH) AF: 0.561 AC: 1182 AN: 2108

Alfa AF: 0.553 Hom.: 5519

Bravo AF: 0.521

Asia WGS AF: 0.654 AC: 2277 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.1
DANN	Benign	0.61
PhyloP100		-0.37

Splicing

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

Other links and lift over

dbSNP: rs2249632; hg19: chr1-209605102;