rs1327872

Positions:

• chr1-190564570-G-A

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 0.134 in 152,022 control chromosomes in the GnomAD database, including 1,568 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 0.13 (1568 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.43

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.186 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: 0.134 AC: 20300 AN: 151904 Hom.: 1557 Cov.: 32

Gnomad AFR AF: 0.0670

Gnomad AMI AF: 0.237

Gnomad AMR AF: 0.190

Gnomad ASJ AF: 0.104

Gnomad EAS AF: 0.169

Gnomad SAS AF: 0.0965

Gnomad FIN AF: 0.186

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.153

Gnomad OTH AF: 0.132

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

GnomAD4 genome AF: 0.134 AC: 20324 AN: 152022 Hom.: 1568 Cov.: 32 AF XY: 0.135 AC XY: 10054 AN XY: 74272

Gnomad4 AFR AF: 0.0672

Gnomad4 AMR AF: 0.191

Gnomad4 ASJ AF: 0.104

Gnomad4 EAS AF: 0.169

Gnomad4 SAS AF: 0.0961

Gnomad4 FIN AF: 0.186

Gnomad4 NFE AF: 0.153

Gnomad4 OTH AF: 0.131

Alfa AF: 0.149 Hom.: 3638

Bravo AF: 0.136

Asia WGS AF: 0.132 AC: 459 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.25
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1327872; hg19: chr1-190533700;