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. The variant received -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
• Publications: 7 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.211 AC: 8729 AN: 41464

American (AMR) AF: 0.296 AC: 4521 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.232 AC: 803 AN: 3466

East Asian (EAS) AF: 0.284 AC: 1467 AN: 5164

South Asian (SAS) AF: 0.322 AC: 1549 AN: 4812

European-Finnish (FIN) AF: 0.420 AC: 4415 AN: 10512

Middle Eastern (MID) AF: 0.293 AC: 86 AN: 294

European-Non Finnish (NFE) AF: 0.381 AC: 25910 AN: 67940

Other (OTH) AF: 0.308 AC: 647 AN: 2102

Alfa AF: 0.350 Hom.: 30074

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
PhyloP100		0.012

Splicing

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

Other links and lift over

dbSNP: rs1780436; hg19: chr10-34257612;