chr10-77767860-G-A

Position:

• chr10-77767860-G-A

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 0.257 in 152,106 control chromosomes in the GnomAD database, including 5,602 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 (5602 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.141

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.384 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.257 AC: 39073 AN: 151988 Hom.: 5590 Cov.: 32

Gnomad AFR AF: 0.150

Gnomad AMI AF: 0.202

Gnomad AMR AF: 0.392

Gnomad ASJ AF: 0.187

Gnomad EAS AF: 0.303

Gnomad SAS AF: 0.304

Gnomad FIN AF: 0.309

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.282

Gnomad OTH AF: 0.252

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

GnomAD4 genome AF: 0.257 AC: 39116 AN: 152106 Hom.: 5602 Cov.: 32 AF XY: 0.262 AC XY: 19468 AN XY: 74330

Gnomad4 AFR AF: 0.150

Gnomad4 AMR AF: 0.393

Gnomad4 ASJ AF: 0.187

Gnomad4 EAS AF: 0.302

Gnomad4 SAS AF: 0.305

Gnomad4 FIN AF: 0.309

Gnomad4 NFE AF: 0.282

Gnomad4 OTH AF: 0.251

Alfa AF: 0.156 Hom.: 341

Bravo AF: 0.257

Asia WGS AF: 0.316 AC: 1101 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.1
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1344967; hg19: chr10-79527618;