rs1324491

Variant names:

• chr1-59884944-G-A
• rs1324491

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 0.179 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
• Publications: 1 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 (AFR) allele frequency at 95% confidence interval = 0.317 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.322 AC: 13338 AN: 41432

American (AMR) AF: 0.154 AC: 2359 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.0720 AC: 250 AN: 3472

East Asian (EAS) AF: 0.128 AC: 664 AN: 5168

South Asian (SAS) AF: 0.0954 AC: 460 AN: 4822

European-Finnish (FIN) AF: 0.127 AC: 1347 AN: 10584

Middle Eastern (MID) AF: 0.112 AC: 33 AN: 294

European-Non Finnish (NFE) AF: 0.125 AC: 8507 AN: 67984

Other (OTH) AF: 0.149 AC: 314 AN: 2112

Alfa AF: 0.156 Hom.: 300

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
PhyloP100		-0.27

Splicing

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

Other links and lift over

dbSNP: rs1324491; hg19: chr1-60350616;