10-67875768-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 0.627 in 152,028 control chromosomes in the GnomAD database, including 30,735 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 0.63 (30735 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0150

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.673 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: 0.627 AC: 95249 AN: 151908 Hom.: 30714 Cov.: 32

Gnomad AFR AF: 0.649

Gnomad AMI AF: 0.527

Gnomad AMR AF: 0.571

Gnomad ASJ AF: 0.685

Gnomad EAS AF: 0.152

Gnomad SAS AF: 0.455

Gnomad FIN AF: 0.591

Gnomad MID AF: 0.636

Gnomad NFE AF: 0.678

Gnomad OTH AF: 0.624

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

GnomAD4 genome AF: 0.627 AC: 95311 AN: 152028 Hom.: 30735 Cov.: 32 AF XY: 0.618 AC XY: 45897 AN XY: 74312

Gnomad4 AFR AF: 0.649

Gnomad4 AMR AF: 0.570

Gnomad4 ASJ AF: 0.685

Gnomad4 EAS AF: 0.151

Gnomad4 SAS AF: 0.455

Gnomad4 FIN AF: 0.591

Gnomad4 NFE AF: 0.678

Gnomad4 OTH AF: 0.627

Alfa AF: 0.650 Hom.: 3840

Bravo AF: 0.622

Asia WGS AF: 0.390 AC: 1359 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	6.7
Dann	Benign	0.88

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7894483; hg19: chr10-69635526;