1-200206940-G-A

Variant names:

• chr1-200206940-G-A
• rs10919843

Variant summary

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

The variant allele was found at a frequency of 0.482 in 151,908 control chromosomes in the GnomAD database, including 20,527 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 0.48 (20527 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.320
• Publications: 5 publications found

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 (AFR) allele frequency at 95% confidence interval = 0.739 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: 0.482 AC: 73172 AN: 151790 Hom.: 20481 Cov.: 31

Gnomad AFR AF: 0.746

Gnomad AMI AF: 0.331

Gnomad AMR AF: 0.525

Gnomad ASJ AF: 0.429

Gnomad EAS AF: 0.705

Gnomad SAS AF: 0.523

Gnomad FIN AF: 0.319

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.322

Gnomad OTH AF: 0.491

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

GnomAD4 genome AF: 0.482 AC: 73271 AN: 151908 Hom.: 20527 Cov.: 31 AF XY: 0.486 AC XY: 36065 AN XY: 74212

African (AFR) AF: 0.746 AC: 30900 AN: 41396

American (AMR) AF: 0.525 AC: 8021 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.429 AC: 1485 AN: 3462

East Asian (EAS) AF: 0.705 AC: 3652 AN: 5178

South Asian (SAS) AF: 0.523 AC: 2521 AN: 4818

European-Finnish (FIN) AF: 0.319 AC: 3347 AN: 10508

Middle Eastern (MID) AF: 0.473 AC: 139 AN: 294

European-Non Finnish (NFE) AF: 0.322 AC: 21878 AN: 67958

Other (OTH) AF: 0.486 AC: 1026 AN: 2112

Alfa AF: 0.376 Hom.: 36159

Bravo AF: 0.514

Asia WGS AF: 0.590 AC: 2054 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.32

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs10919843; hg19: chr1-200176068;