rs11196260

Positions:

• chr10-113185119-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The variant allele was found at a frequency of 0.0245 in 152,280 control chromosomes in the GnomAD database, including 69 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 0.025 (69 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.61

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0245 (3738/152280) while in subpopulation NFE AF= 0.0378 (2568/68020). AF 95% confidence interval is 0.0365. There are 69 homozygotes in gnomad4. There are 1663 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 69 gene

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: 0.0246 AC: 3741 AN: 152162 Hom.: 69 Cov.: 32

Gnomad AFR AF: 0.0111

Gnomad AMI AF: 0.0263

Gnomad AMR AF: 0.0179

Gnomad ASJ AF: 0.0461

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.0182

Gnomad FIN AF: 0.00669

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.0378

Gnomad OTH AF: 0.0321

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

GnomAD4 genome AF: 0.0245 AC: 3738 AN: 152280 Hom.: 69 Cov.: 32 AF XY: 0.0223 AC XY: 1663 AN XY: 74474

Gnomad4 AFR AF: 0.0111

Gnomad4 AMR AF: 0.0178

Gnomad4 ASJ AF: 0.0461

Gnomad4 EAS AF: 0.000386

Gnomad4 SAS AF: 0.0182

Gnomad4 FIN AF: 0.00669

Gnomad4 NFE AF: 0.0378

Gnomad4 OTH AF: 0.0318

Alfa AF: 0.0285 Hom.: 6

Bravo AF: 0.0246

Asia WGS AF: 0.00751 AC: 26 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	8.0
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11196260; hg19: chr10-114944878;