1-1163962-A-C

Variant names:

• chr1-1163962-A-C
• rs9660710
• XR_007065348.1:n.710A>C

Variant summary

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

The XR_007065348.1(MIR200BHG):​n.710A>C 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 0.883 in 152,042 control chromosomes in the GnomAD database, including 59,693 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 0.88 (59693 hom., cov: 30)
• Consequence: MIR200BHG XR_007065348.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.280
• Publications: 13 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=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.924 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.883 AC: 134080 AN: 151924 Hom.: 59641 Cov.: 30

Gnomad AFR AF: 0.827

Gnomad AMI AF: 0.990

Gnomad AMR AF: 0.900

Gnomad ASJ AF: 0.910

Gnomad EAS AF: 0.575

Gnomad SAS AF: 0.885

Gnomad FIN AF: 0.899

Gnomad MID AF: 0.949

Gnomad NFE AF: 0.930

Gnomad OTH AF: 0.877

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

GnomAD4 genome AF: 0.883 AC: 134189 AN: 152042 Hom.: 59693 Cov.: 30 AF XY: 0.880 AC XY: 65421 AN XY: 74316

African (AFR) AF: 0.827 AC: 34255 AN: 41438

American (AMR) AF: 0.900 AC: 13764 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.910 AC: 3159 AN: 3472

East Asian (EAS) AF: 0.576 AC: 2957 AN: 5136

South Asian (SAS) AF: 0.885 AC: 4258 AN: 4814

European-Finnish (FIN) AF: 0.899 AC: 9527 AN: 10592

Middle Eastern (MID) AF: 0.946 AC: 278 AN: 294

European-Non Finnish (NFE) AF: 0.930 AC: 63236 AN: 67984

Other (OTH) AF: 0.877 AC: 1854 AN: 2114

Alfa AF: 0.912 Hom.: 112460

Bravo AF: 0.876

Asia WGS AF: 0.736 AC: 2560 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.4
DANN	Benign	0.36
PhyloP100		-0.28

Splicing

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

Other links and lift over

dbSNP: rs9660710; hg19: chr1-1099342;