1-203212297-A-G

Variant names:

• chr1-203212297-A-G
• rs4950936

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 0.494 in 152,098 control chromosomes in the GnomAD database, including 19,662 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 0.49 (19662 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.442
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.939 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: 0.494 AC: 75110 AN: 151980 Hom.: 19642 Cov.: 33

Gnomad AFR AF: 0.392

Gnomad AMI AF: 0.326

Gnomad AMR AF: 0.614

Gnomad ASJ AF: 0.515

Gnomad EAS AF: 0.961

Gnomad SAS AF: 0.717

Gnomad FIN AF: 0.491

Gnomad MID AF: 0.472

Gnomad NFE AF: 0.479

Gnomad OTH AF: 0.519

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

GnomAD4 genome AF: 0.494 AC: 75173 AN: 152098 Hom.: 19662 Cov.: 33 AF XY: 0.505 AC XY: 37571 AN XY: 74362

African (AFR) AF: 0.392 AC: 16247 AN: 41488

American (AMR) AF: 0.614 AC: 9394 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.515 AC: 1787 AN: 3470

East Asian (EAS) AF: 0.961 AC: 4968 AN: 5170

South Asian (SAS) AF: 0.716 AC: 3457 AN: 4830

European-Finnish (FIN) AF: 0.491 AC: 5194 AN: 10578

Middle Eastern (MID) AF: 0.476 AC: 140 AN: 294

European-Non Finnish (NFE) AF: 0.480 AC: 32586 AN: 67958

Other (OTH) AF: 0.522 AC: 1103 AN: 2112

Alfa AF: 0.486 Hom.: 2263

Bravo AF: 0.496

Asia WGS AF: 0.806 AC: 2797 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.8
DANN	Benign	0.65
PhyloP100		-0.44

Splicing

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

Other links and lift over

dbSNP: rs4950936; hg19: chr1-203181425;