rs764851

chr10-6005981-A-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 0.108 in 152,200 control chromosomes in the GnomAD database, including 1,122 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 0.11 (1122 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.344

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.156 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: 0.108 AC: 16430 AN: 152082 Hom.: 1125 Cov.: 30

Gnomad AFR AF: 0.0283

Gnomad AMI AF: 0.0614

Gnomad AMR AF: 0.0738

Gnomad ASJ AF: 0.118

Gnomad EAS AF: 0.132

Gnomad SAS AF: 0.166

Gnomad FIN AF: 0.120

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.157

Gnomad OTH AF: 0.106

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

GnomAD4 genome AF: 0.108 AC: 16417 AN: 152200 Hom.: 1122 Cov.: 30 AF XY: 0.106 AC XY: 7862 AN XY: 74416

Gnomad4 AFR AF: 0.0283

Gnomad4 AMR AF: 0.0737

Gnomad4 ASJ AF: 0.118

Gnomad4 EAS AF: 0.131

Gnomad4 SAS AF: 0.166

Gnomad4 FIN AF: 0.120

Gnomad4 NFE AF: 0.157

Gnomad4 OTH AF: 0.105

Alfa AF: 0.132 Hom.: 176

Bravo AF: 0.0996

Asia WGS AF: 0.153 AC: 533 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	2.6
Dann	Benign	0.87

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs764851; hg19: chr10-6047944;