rs11599418

Variant names:

• chr10-111659201-T-C
• rs11599418

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 0.277 in 152,122 control chromosomes in the GnomAD database, including 7,162 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 0.28 (7162 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.19
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.379 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: 0.278 AC: 42208 AN: 152004 Hom.: 7164 Cov.: 33

Gnomad AFR AF: 0.116

Gnomad AMI AF: 0.384

Gnomad AMR AF: 0.237

Gnomad ASJ AF: 0.363

Gnomad EAS AF: 0.0152

Gnomad SAS AF: 0.201

Gnomad FIN AF: 0.413

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.383

Gnomad OTH AF: 0.291

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

GnomAD4 genome AF: 0.277 AC: 42213 AN: 152122 Hom.: 7162 Cov.: 33 AF XY: 0.275 AC XY: 20463 AN XY: 74370

African (AFR) AF: 0.116 AC: 4830 AN: 41516

American (AMR) AF: 0.237 AC: 3614 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.363 AC: 1260 AN: 3468

East Asian (EAS) AF: 0.0152 AC: 79 AN: 5182

South Asian (SAS) AF: 0.203 AC: 977 AN: 4822

European-Finnish (FIN) AF: 0.413 AC: 4360 AN: 10556

Middle Eastern (MID) AF: 0.296 AC: 87 AN: 294

European-Non Finnish (NFE) AF: 0.383 AC: 26051 AN: 67988

Other (OTH) AF: 0.287 AC: 605 AN: 2110

Alfa AF: 0.313 Hom.: 1378

Bravo AF: 0.258

Asia WGS AF: 0.0920 AC: 321 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.078
DANN	Benign	0.76
PhyloP100		-3.2

Splicing

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

Other links and lift over

dbSNP: rs11599418; hg19: chr10-113418959;