chr10-67920067-T-C

Position:

• chr10-67920067-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 0.633 in 152,088 control chromosomes in the GnomAD database, including 31,336 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 (31336 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.181

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 (NFE) allele frequency at 95% confidence interval = 0.673 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: 0.633 AC: 96186 AN: 151968 Hom.: 31310 Cov.: 32

Gnomad AFR AF: 0.671

Gnomad AMI AF: 0.529

Gnomad AMR AF: 0.573

Gnomad ASJ AF: 0.686

Gnomad EAS AF: 0.152

Gnomad SAS AF: 0.454

Gnomad FIN AF: 0.590

Gnomad MID AF: 0.634

Gnomad NFE AF: 0.678

Gnomad OTH AF: 0.633

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

GnomAD4 genome AF: 0.633 AC: 96255 AN: 152088 Hom.: 31336 Cov.: 32 AF XY: 0.623 AC XY: 46335 AN XY: 74350

Gnomad4 AFR AF: 0.671

Gnomad4 AMR AF: 0.572

Gnomad4 ASJ AF: 0.686

Gnomad4 EAS AF: 0.152

Gnomad4 SAS AF: 0.454

Gnomad4 FIN AF: 0.590

Gnomad4 NFE AF: 0.678

Gnomad4 OTH AF: 0.636

Alfa AF: 0.646 Hom.: 2778

Bravo AF: 0.629

Asia WGS AF: 0.389 AC: 1357 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.9
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10997875; hg19: chr10-69679824;