XR_007065348.1:n.382+76C>G

Variant names:

• chr1-1163334-C-G
• rs4379629
• XR_007065348.1:n.382+76C>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.382+76C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.495 in 152,092 control chromosomes in the GnomAD database, including 20,011 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 0.50 (20011 hom., cov: 34)
• Consequence: MIR200BHG XR_007065348.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.300
• 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=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.628 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.495 AC: 75266 AN: 151974 Hom.: 20001 Cov.: 34

Gnomad AFR AF: 0.323

Gnomad AMI AF: 0.660

Gnomad AMR AF: 0.638

Gnomad ASJ AF: 0.601

Gnomad EAS AF: 0.287

Gnomad SAS AF: 0.450

Gnomad FIN AF: 0.473

Gnomad MID AF: 0.561

Gnomad NFE AF: 0.581

Gnomad OTH AF: 0.531

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

GnomAD4 genome AF: 0.495 AC: 75304 AN: 152092 Hom.: 20011 Cov.: 34 AF XY: 0.489 AC XY: 36392 AN XY: 74350

African (AFR) AF: 0.323 AC: 13423 AN: 41512

American (AMR) AF: 0.639 AC: 9768 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.601 AC: 2086 AN: 3470

East Asian (EAS) AF: 0.288 AC: 1486 AN: 5152

South Asian (SAS) AF: 0.450 AC: 2174 AN: 4828

European-Finnish (FIN) AF: 0.473 AC: 5012 AN: 10600

Middle Eastern (MID) AF: 0.558 AC: 163 AN: 292

European-Non Finnish (NFE) AF: 0.581 AC: 39479 AN: 67918

Other (OTH) AF: 0.526 AC: 1111 AN: 2112

Alfa AF: 0.372 Hom.: 993

Bravo AF: 0.500

Asia WGS AF: 0.367 AC: 1281 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.6
DANN	Benign	0.41
PhyloP100		-0.30

Splicing

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

Other links and lift over

dbSNP: rs4379629; hg19: chr1-1098714;