rs1034200

Variant names:

• chr13-22654552-C-A
• rs1034200

Your query was ambiguous. Multiple possible variants found:

• chr13-22654552-C-A
• chr13-22654552-C-T

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 0.382 in 151,994 control chromosomes in the GnomAD database, including 12,618 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 (12618 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0720

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.592 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: 0.382 AC: 58005 AN: 151874 Hom.: 12595 Cov.: 32

Gnomad AFR AF: 0.598

Gnomad AMI AF: 0.221

Gnomad AMR AF: 0.301

Gnomad ASJ AF: 0.251

Gnomad EAS AF: 0.334

Gnomad SAS AF: 0.213

Gnomad FIN AF: 0.413

Gnomad MID AF: 0.318

Gnomad NFE AF: 0.289

Gnomad OTH AF: 0.356

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

GnomAD4 genome AF: 0.382 AC: 58076 AN: 151994 Hom.: 12618 Cov.: 32 AF XY: 0.382 AC XY: 28371 AN XY: 74290

Gnomad4 AFR AF: 0.598

Gnomad4 AMR AF: 0.300

Gnomad4 ASJ AF: 0.251

Gnomad4 EAS AF: 0.334

Gnomad4 SAS AF: 0.213

Gnomad4 FIN AF: 0.413

Gnomad4 NFE AF: 0.289

Gnomad4 OTH AF: 0.357

Alfa AF: 0.288 Hom.: 14914

Bravo AF: 0.382

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.8
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1034200; hg19: chr13-23228691;