rs11110700

Positions:

• chr12-101217260-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 0.155 in 152,202 control chromosomes in the GnomAD database, including 2,248 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 0.16 (2248 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.953

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.319 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.155 AC: 23620 AN: 152084 Hom.: 2246 Cov.: 32

Gnomad AFR AF: 0.0553

Gnomad AMI AF: 0.305

Gnomad AMR AF: 0.131

Gnomad ASJ AF: 0.214

Gnomad EAS AF: 0.149

Gnomad SAS AF: 0.332

Gnomad FIN AF: 0.144

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.206

Gnomad OTH AF: 0.168

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

GnomAD4 genome AF: 0.155 AC: 23619 AN: 152202 Hom.: 2248 Cov.: 32 AF XY: 0.154 AC XY: 11479 AN XY: 74416

Gnomad4 AFR AF: 0.0552

Gnomad4 AMR AF: 0.131

Gnomad4 ASJ AF: 0.214

Gnomad4 EAS AF: 0.149

Gnomad4 SAS AF: 0.332

Gnomad4 FIN AF: 0.144

Gnomad4 NFE AF: 0.206

Gnomad4 OTH AF: 0.171

Alfa AF: 0.190 Hom.: 2346

Bravo AF: 0.145

Asia WGS AF: 0.245 AC: 853 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	3.4
DANN	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11110700; hg19: chr12-101611038;