1-209431757-A-T

Variant names:

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

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000429156.7(MIR205HG):​n.594A>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
• 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).

Transcripts

RefSeq

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

Ensembl

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

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 0

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.90
DANN	Benign	0.76
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;