XR_007065348.1:n.102C>G

Variant names:

• chr1-1162978-C-G
• rs61768479
• XR_007065348.1:n.102C>G

Variant summary

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

The XR_007065348.1(MIR200BHG):​n.102C>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 0.0449 in 152,352 control chromosomes in the GnomAD database, including 224 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 0.045 (224 hom., cov: 34)
• Consequence: MIR200BHG XR_007065348.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.600
• Publications: 2 publications found

Genes affected

MIR200BHG (HGNC:58145):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0675 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MIR200BHG	XR_007065348.1	n.102C>G		non_coding_transcript_exon_variant	Exon 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0449 AC: 6842 AN: 152234 Hom.: 224 Cov.: 34

Gnomad AFR AF: 0.0107

Gnomad AMI AF: 0.0735

Gnomad AMR AF: 0.0247

Gnomad ASJ AF: 0.0144

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.0136

Gnomad FIN AF: 0.100

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.0691

Gnomad OTH AF: 0.0315

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

GnomAD4 genome AF: 0.0449 AC: 6838 AN: 152352 Hom.: 224 Cov.: 34 AF XY: 0.0455 AC XY: 3386 AN XY: 74494

African (AFR) AF: 0.0107 AC: 444 AN: 41588

American (AMR) AF: 0.0246 AC: 377 AN: 15312

Ashkenazi Jewish (ASJ) AF: 0.0144 AC: 50 AN: 3472

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5190

South Asian (SAS) AF: 0.0135 AC: 65 AN: 4832

European-Finnish (FIN) AF: 0.100 AC: 1065 AN: 10622

Middle Eastern (MID) AF: 0.0102 AC: 3 AN: 294

European-Non Finnish (NFE) AF: 0.0691 AC: 4701 AN: 68014

Other (OTH) AF: 0.0307 AC: 65 AN: 2116

Alfa AF: 0.0612 Hom.: 47

Bravo AF: 0.0377

Asia WGS AF: 0.00664 AC: 23 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	1.5
DANN	Benign	0.29
PhyloP100		-0.60

Splicing

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

Other links and lift over

dbSNP: rs61768479; hg19: chr1-1098358;