rs1324491

Positions:

• chr1-59884944-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 0.179 in 152,058 control chromosomes in the GnomAD database, including 3,076 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 0.18 (3076 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.267

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 (AFR) allele frequency at 95% confidence interval = 0.317 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: 0.179 AC: 27248 AN: 151940 Hom.: 3063 Cov.: 32

Gnomad AFR AF: 0.322

Gnomad AMI AF: 0.0230

Gnomad AMR AF: 0.154

Gnomad ASJ AF: 0.0720

Gnomad EAS AF: 0.129

Gnomad SAS AF: 0.0961

Gnomad FIN AF: 0.127

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.125

Gnomad OTH AF: 0.149

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

GnomAD4 genome AF: 0.179 AC: 27293 AN: 152058 Hom.: 3076 Cov.: 32 AF XY: 0.177 AC XY: 13186 AN XY: 74342

Gnomad4 AFR AF: 0.322

Gnomad4 AMR AF: 0.154

Gnomad4 ASJ AF: 0.0720

Gnomad4 EAS AF: 0.128

Gnomad4 SAS AF: 0.0954

Gnomad4 FIN AF: 0.127

Gnomad4 NFE AF: 0.125

Gnomad4 OTH AF: 0.149

Alfa AF: 0.150 Hom.: 272

Bravo AF: 0.185

Asia WGS AF: 0.138 AC: 479 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	1.2
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1324491; hg19: chr1-60350616;