rs10403561

Variant names:

• chr19-33299596-A-G
• rs10403561

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 0.464 in 151,938 control chromosomes in the GnomAD database, including 16,851 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 0.46 (16851 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.404

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.576 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: 0.463 AC: 70359 AN: 151820 Hom.: 16809 Cov.: 32

Gnomad AFR AF: 0.582

Gnomad AMI AF: 0.553

Gnomad AMR AF: 0.393

Gnomad ASJ AF: 0.407

Gnomad EAS AF: 0.460

Gnomad SAS AF: 0.426

Gnomad FIN AF: 0.372

Gnomad MID AF: 0.437

Gnomad NFE AF: 0.426

Gnomad OTH AF: 0.464

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

GnomAD4 genome AF: 0.464 AC: 70445 AN: 151938 Hom.: 16851 Cov.: 32 AF XY: 0.460 AC XY: 34124 AN XY: 74262

Gnomad4 AFR AF: 0.582

Gnomad4 AMR AF: 0.393

Gnomad4 ASJ AF: 0.407

Gnomad4 EAS AF: 0.461

Gnomad4 SAS AF: 0.428

Gnomad4 FIN AF: 0.372

Gnomad4 NFE AF: 0.426

Gnomad4 OTH AF: 0.459

Alfa AF: 0.438 Hom.: 10430

Bravo AF: 0.471

Asia WGS AF: 0.434 AC: 1513 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	8.3
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10403561; hg19: chr19-33790502;