rs1021188

Variant names:

• chr13-42541997-C-T
• rs1021188

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 0.793 in 152,174 control chromosomes in the GnomAD database, including 48,086 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 0.79 (48086 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.653
• Publications: 33 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.854 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: 0.793 AC: 120598 AN: 152056 Hom.: 48051 Cov.: 32

Gnomad AFR AF: 0.754

Gnomad AMI AF: 0.802

Gnomad AMR AF: 0.689

Gnomad ASJ AF: 0.813

Gnomad EAS AF: 0.731

Gnomad SAS AF: 0.877

Gnomad FIN AF: 0.871

Gnomad MID AF: 0.813

Gnomad NFE AF: 0.826

Gnomad OTH AF: 0.797

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

GnomAD4 genome AF: 0.793 AC: 120676 AN: 152174 Hom.: 48086 Cov.: 32 AF XY: 0.794 AC XY: 59102 AN XY: 74404

African (AFR) AF: 0.754 AC: 31284 AN: 41494

American (AMR) AF: 0.688 AC: 10517 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.813 AC: 2821 AN: 3470

East Asian (EAS) AF: 0.731 AC: 3786 AN: 5176

South Asian (SAS) AF: 0.876 AC: 4216 AN: 4814

European-Finnish (FIN) AF: 0.871 AC: 9233 AN: 10602

Middle Eastern (MID) AF: 0.830 AC: 244 AN: 294

European-Non Finnish (NFE) AF: 0.826 AC: 56154 AN: 68010

Other (OTH) AF: 0.799 AC: 1690 AN: 2114

Alfa AF: 0.813 Hom.: 190580

Bravo AF: 0.773

Asia WGS AF: 0.800 AC: 2781 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.27
DANN	Benign	0.21
PhyloP100		-0.65

Splicing

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

Other links and lift over

dbSNP: rs1021188; hg19: chr13-43116133;