10-67920067-T-C

Variant names:

• chr10-67920067-T-C
• rs10997875

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 28 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.671 AC: 27814 AN: 41482

American (AMR) AF: 0.572 AC: 8729 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.686 AC: 2382 AN: 3470

East Asian (EAS) AF: 0.152 AC: 787 AN: 5182

South Asian (SAS) AF: 0.454 AC: 2192 AN: 4828

European-Finnish (FIN) AF: 0.590 AC: 6229 AN: 10552

Middle Eastern (MID) AF: 0.633 AC: 186 AN: 294

European-Non Finnish (NFE) AF: 0.678 AC: 46110 AN: 67982

Other (OTH) AF: 0.636 AC: 1344 AN: 2114

Alfa AF: 0.664 Hom.: 41868

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
PhyloP100		0.18

Splicing

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

Other links and lift over

dbSNP: rs10997875; hg19: chr10-69679824;