1-209815925-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.834 in 152,080 control chromosomes in the GnomAD database, including 52,996 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 0.83 (52996 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.778

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.89 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.834 AC: 126679 AN: 151962 Hom.: 52956 Cov.: 30

Gnomad AFR AF: 0.898

Gnomad AMI AF: 0.862

Gnomad AMR AF: 0.841

Gnomad ASJ AF: 0.812

Gnomad EAS AF: 0.809

Gnomad SAS AF: 0.786

Gnomad FIN AF: 0.777

Gnomad MID AF: 0.822

Gnomad NFE AF: 0.808

Gnomad OTH AF: 0.839

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

GnomAD4 genome AF: 0.834 AC: 126777 AN: 152080 Hom.: 52996 Cov.: 30 AF XY: 0.831 AC XY: 61744 AN XY: 74326

Gnomad4 AFR AF: 0.898

Gnomad4 AMR AF: 0.840

Gnomad4 ASJ AF: 0.812

Gnomad4 EAS AF: 0.809

Gnomad4 SAS AF: 0.785

Gnomad4 FIN AF: 0.777

Gnomad4 NFE AF: 0.808

Gnomad4 OTH AF: 0.835

Alfa AF: 0.813 Hom.: 89912

Bravo AF: 0.839

Asia WGS AF: 0.766 AC: 2667 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	14
Dann	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs642961; hg19: chr1-209989270;