10-4282231-G-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 0.621 in 152,066 control chromosomes in the GnomAD database, including 30,204 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 0.62 (30204 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.393

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.659 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: 0.621 AC: 94409 AN: 151948 Hom.: 30187 Cov.: 32

Gnomad AFR AF: 0.608

Gnomad AMI AF: 0.647

Gnomad AMR AF: 0.608

Gnomad ASJ AF: 0.652

Gnomad EAS AF: 0.123

Gnomad SAS AF: 0.466

Gnomad FIN AF: 0.717

Gnomad MID AF: 0.655

Gnomad NFE AF: 0.664

Gnomad OTH AF: 0.634

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

GnomAD4 genome AF: 0.621 AC: 94467 AN: 152066 Hom.: 30204 Cov.: 32 AF XY: 0.619 AC XY: 46032 AN XY: 74328

Gnomad4 AFR AF: 0.608

Gnomad4 AMR AF: 0.607

Gnomad4 ASJ AF: 0.652

Gnomad4 EAS AF: 0.123

Gnomad4 SAS AF: 0.467

Gnomad4 FIN AF: 0.717

Gnomad4 NFE AF: 0.664

Gnomad4 OTH AF: 0.633

Alfa AF: 0.576 Hom.: 1885

Bravo AF: 0.607

Asia WGS AF: 0.354 AC: 1233 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	1.1
Dann	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1022768; hg19: chr10-4324423;