chr10-123245677-C-T

Variant names:

• chr10-123245677-C-T
• rs17663978

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 0.0899 in 152,242 control chromosomes in the GnomAD database, including 678 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 0.090 (678 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.347
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.109 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: 0.0899 AC: 13679 AN: 152122 Hom.: 677 Cov.: 32

Gnomad AFR AF: 0.0717

Gnomad AMI AF: 0.179

Gnomad AMR AF: 0.0886

Gnomad ASJ AF: 0.0971

Gnomad EAS AF: 0.0439

Gnomad SAS AF: 0.117

Gnomad FIN AF: 0.109

Gnomad MID AF: 0.162

Gnomad NFE AF: 0.0977

Gnomad OTH AF: 0.100

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

GnomAD4 genome AF: 0.0899 AC: 13681 AN: 152242 Hom.: 678 Cov.: 32 AF XY: 0.0913 AC XY: 6794 AN XY: 74452

African (AFR) AF: 0.0716 AC: 2974 AN: 41538

American (AMR) AF: 0.0883 AC: 1351 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0971 AC: 337 AN: 3470

East Asian (EAS) AF: 0.0436 AC: 226 AN: 5182

South Asian (SAS) AF: 0.117 AC: 563 AN: 4828

European-Finnish (FIN) AF: 0.109 AC: 1157 AN: 10602

Middle Eastern (MID) AF: 0.173 AC: 51 AN: 294

European-Non Finnish (NFE) AF: 0.0977 AC: 6644 AN: 68012

Other (OTH) AF: 0.102 AC: 215 AN: 2112

Alfa AF: 0.0978 Hom.: 1317

Bravo AF: 0.0862

Asia WGS AF: 0.0780 AC: 270 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.4
DANN	Benign	0.83
PhyloP100		-0.35

Splicing

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

Other links and lift over

dbSNP: rs17663978; hg19: chr10-125005193;