10-8701774-T-C

Variant names:

• chr10-8701774-T-C
• rs1999638

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.153 in 152,166 control chromosomes in the GnomAD database, including 2,029 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 0.15 (2029 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.70

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.21).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.198 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: 0.153 AC: 23315 AN: 152048 Hom.: 2031 Cov.: 32

Gnomad AFR AF: 0.0958

Gnomad AMI AF: 0.179

Gnomad AMR AF: 0.156

Gnomad ASJ AF: 0.162

Gnomad EAS AF: 0.0775

Gnomad SAS AF: 0.103

Gnomad FIN AF: 0.119

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.201

Gnomad OTH AF: 0.170

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

GnomAD4 genome AF: 0.153 AC: 23304 AN: 152166 Hom.: 2029 Cov.: 32 AF XY: 0.150 AC XY: 11127 AN XY: 74418

Gnomad4 AFR AF: 0.0956

Gnomad4 AMR AF: 0.156

Gnomad4 ASJ AF: 0.162

Gnomad4 EAS AF: 0.0774

Gnomad4 SAS AF: 0.102

Gnomad4 FIN AF: 0.119

Gnomad4 NFE AF: 0.201

Gnomad4 OTH AF: 0.168

Alfa AF: 0.173 Hom.: 671

Bravo AF: 0.158

Asia WGS AF: 0.0800 AC: 277 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.21
CADD	Benign	19
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1999638; hg19: chr10-8743737;