chr10-112884177-C-T

Variant names:

• chr10-112884177-C-T
• rs11595716

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 0.337 in 151,944 control chromosomes in the GnomAD database, including 9,191 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 0.34 (9191 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0610
• Publications: 5 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 (AFR) allele frequency at 95% confidence interval = 0.409 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: 0.337 AC: 51160 AN: 151826 Hom.: 9167 Cov.: 32

Gnomad AFR AF: 0.413

Gnomad AMI AF: 0.308

Gnomad AMR AF: 0.280

Gnomad ASJ AF: 0.389

Gnomad EAS AF: 0.0259

Gnomad SAS AF: 0.230

Gnomad FIN AF: 0.352

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.329

Gnomad OTH AF: 0.356

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

GnomAD4 genome AF: 0.337 AC: 51227 AN: 151944 Hom.: 9191 Cov.: 32 AF XY: 0.335 AC XY: 24858 AN XY: 74268

African (AFR) AF: 0.414 AC: 17150 AN: 41420

American (AMR) AF: 0.280 AC: 4268 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.389 AC: 1348 AN: 3468

East Asian (EAS) AF: 0.0259 AC: 134 AN: 5170

South Asian (SAS) AF: 0.229 AC: 1105 AN: 4820

European-Finnish (FIN) AF: 0.352 AC: 3708 AN: 10544

Middle Eastern (MID) AF: 0.378 AC: 111 AN: 294

European-Non Finnish (NFE) AF: 0.329 AC: 22380 AN: 67946

Other (OTH) AF: 0.352 AC: 743 AN: 2112

Alfa AF: 0.327 Hom.: 4363

Bravo AF: 0.335

Asia WGS AF: 0.132 AC: 462 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	5.5
DANN	Benign	0.75
PhyloP100		-0.061

Splicing

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

Other links and lift over

dbSNP: rs11595716; hg19: chr10-114643936;