rs1780436

Variant names:

• chr10-33968684-G-A
• rs1780436

Your query was ambiguous. Multiple possible variants found:

• chr10-33968684-G-A
• chr10-33968684-G-C
• chr10-33968684-G-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 0.319 in 151,924 control chromosomes in the GnomAD database, including 8,196 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 0.32 (8196 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0120

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.377 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: 0.319 AC: 48352 AN: 151806 Hom.: 8188 Cov.: 31

Gnomad AFR AF: 0.211

Gnomad AMI AF: 0.290

Gnomad AMR AF: 0.296

Gnomad ASJ AF: 0.232

Gnomad EAS AF: 0.284

Gnomad SAS AF: 0.321

Gnomad FIN AF: 0.420

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.381

Gnomad OTH AF: 0.305

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

GnomAD4 genome AF: 0.319 AC: 48390 AN: 151924 Hom.: 8196 Cov.: 31 AF XY: 0.320 AC XY: 23774 AN XY: 74236

Gnomad4 AFR AF: 0.211

Gnomad4 AMR AF: 0.296

Gnomad4 ASJ AF: 0.232

Gnomad4 EAS AF: 0.284

Gnomad4 SAS AF: 0.322

Gnomad4 FIN AF: 0.420

Gnomad4 NFE AF: 0.381

Gnomad4 OTH AF: 0.308

Alfa AF: 0.359 Hom.: 12098

Bravo AF: 0.298

Asia WGS AF: 0.271 AC: 946 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.97
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1780436; hg19: chr10-34257612;