10-111764613-T-C

Position:

• chr10-111764613-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 0.842 in 152,106 control chromosomes in the GnomAD database, including 54,880 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 0.84 (54880 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.147

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.927 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: 0.842 AC: 128017 AN: 151988 Hom.: 54859 Cov.: 32

Gnomad AFR AF: 0.674

Gnomad AMI AF: 0.955

Gnomad AMR AF: 0.853

Gnomad ASJ AF: 0.878

Gnomad EAS AF: 0.801

Gnomad SAS AF: 0.763

Gnomad FIN AF: 0.935

Gnomad MID AF: 0.861

Gnomad NFE AF: 0.933

Gnomad OTH AF: 0.854

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

GnomAD4 genome AF: 0.842 AC: 128084 AN: 152106 Hom.: 54880 Cov.: 32 AF XY: 0.842 AC XY: 62577 AN XY: 74346

Gnomad4 AFR AF: 0.674

Gnomad4 AMR AF: 0.852

Gnomad4 ASJ AF: 0.878

Gnomad4 EAS AF: 0.801

Gnomad4 SAS AF: 0.765

Gnomad4 FIN AF: 0.935

Gnomad4 NFE AF: 0.933

Gnomad4 OTH AF: 0.848

Alfa AF: 0.913 Hom.: 98951

Bravo AF: 0.831

Asia WGS AF: 0.763 AC: 2656 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	15
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6585111; hg19: chr10-113524371;