rs1866437

chr10-77767008-T-C

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 0.264 in 152,056 control chromosomes in the GnomAD database, including 6,177 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 0.26 (6177 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.486

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.349 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.264 AC: 40129 AN: 151938 Hom.: 6179 Cov.: 32

Gnomad AFR AF: 0.109

Gnomad AMI AF: 0.462

Gnomad AMR AF: 0.260

Gnomad ASJ AF: 0.374

Gnomad EAS AF: 0.193

Gnomad SAS AF: 0.307

Gnomad FIN AF: 0.264

Gnomad MID AF: 0.339

Gnomad NFE AF: 0.352

Gnomad OTH AF: 0.297

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

GnomAD4 genome AF: 0.264 AC: 40115 AN: 152056 Hom.: 6177 Cov.: 32 AF XY: 0.262 AC XY: 19439 AN XY: 74322

Gnomad4 AFR AF: 0.108

Gnomad4 AMR AF: 0.260

Gnomad4 ASJ AF: 0.374

Gnomad4 EAS AF: 0.192

Gnomad4 SAS AF: 0.307

Gnomad4 FIN AF: 0.264

Gnomad4 NFE AF: 0.352

Gnomad4 OTH AF: 0.293

Alfa AF: 0.319 Hom.: 1737

Bravo AF: 0.256

Asia WGS AF: 0.255 AC: 888 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	0.95
Dann	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1866437; hg19: chr10-79526766;