rs10919202

Positions:

• chr1-169644556-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 0.22 in 152,052 control chromosomes in the GnomAD database, including 4,396 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 0.22 (4396 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.841

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.35 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.220 AC: 33356 AN: 151934 Hom.: 4365 Cov.: 30

Gnomad AFR AF: 0.354

Gnomad AMI AF: 0.181

Gnomad AMR AF: 0.211

Gnomad ASJ AF: 0.140

Gnomad EAS AF: 0.0817

Gnomad SAS AF: 0.241

Gnomad FIN AF: 0.200

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.157

Gnomad OTH AF: 0.213

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

GnomAD4 genome AF: 0.220 AC: 33434 AN: 152052 Hom.: 4396 Cov.: 30 AF XY: 0.221 AC XY: 16456 AN XY: 74324

Gnomad4 AFR AF: 0.355

Gnomad4 AMR AF: 0.211

Gnomad4 ASJ AF: 0.140

Gnomad4 EAS AF: 0.0815

Gnomad4 SAS AF: 0.240

Gnomad4 FIN AF: 0.200

Gnomad4 NFE AF: 0.157

Gnomad4 OTH AF: 0.212

Alfa AF: 0.168 Hom.: 3109

Bravo AF: 0.226

Asia WGS AF: 0.179 AC: 623 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	6.1
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10919202; hg19: chr1-169613794;