rs1321006

Variant names:

• chr20-48437519-C-T
• rs1321006

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 0.381 in 151,980 control chromosomes in the GnomAD database, including 11,344 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 0.38 (11344 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.526
• 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 (AMR) allele frequency at 95% confidence interval = 0.492 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: 0.380 AC: 57774 AN: 151864 Hom.: 11316 Cov.: 32

Gnomad AFR AF: 0.396

Gnomad AMI AF: 0.419

Gnomad AMR AF: 0.501

Gnomad ASJ AF: 0.248

Gnomad EAS AF: 0.476

Gnomad SAS AF: 0.331

Gnomad FIN AF: 0.326

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.356

Gnomad OTH AF: 0.372

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

GnomAD4 genome AF: 0.381 AC: 57848 AN: 151980 Hom.: 11344 Cov.: 32 AF XY: 0.382 AC XY: 28392 AN XY: 74270

African (AFR) AF: 0.396 AC: 16415 AN: 41440

American (AMR) AF: 0.502 AC: 7654 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.248 AC: 860 AN: 3472

East Asian (EAS) AF: 0.476 AC: 2456 AN: 5156

South Asian (SAS) AF: 0.332 AC: 1597 AN: 4810

European-Finnish (FIN) AF: 0.326 AC: 3442 AN: 10554

Middle Eastern (MID) AF: 0.276 AC: 81 AN: 294

European-Non Finnish (NFE) AF: 0.356 AC: 24181 AN: 67976

Other (OTH) AF: 0.370 AC: 780 AN: 2110

Alfa AF: 0.375 Hom.: 1436

Bravo AF: 0.398

Asia WGS AF: 0.384 AC: 1334 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	0.44
DANN	Benign	0.65
PhyloP100		-0.53

Splicing

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

Other links and lift over

dbSNP: rs1321006; hg19: chr20-47066261;