rs11110700

Variant names:

• chr12-101217260-T-C
• rs11110700

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 0.155 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
• Publications: 2 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 (SAS) allele frequency at 95% confidence interval = 0.319 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: 0.155 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

African (AFR) AF: 0.0552 AC: 2295 AN: 41550

American (AMR) AF: 0.131 AC: 2002 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.214 AC: 743 AN: 3472

East Asian (EAS) AF: 0.149 AC: 769 AN: 5170

South Asian (SAS) AF: 0.332 AC: 1599 AN: 4814

European-Finnish (FIN) AF: 0.144 AC: 1522 AN: 10596

Middle Eastern (MID) AF: 0.218 AC: 64 AN: 294

European-Non Finnish (NFE) AF: 0.206 AC: 13986 AN: 67996

Other (OTH) AF: 0.171 AC: 361 AN: 2112

Alfa AF: 0.174 Hom.: 4028

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
PhyloP100		-0.95

Splicing

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

Other links and lift over

dbSNP: rs11110700; hg19: chr12-101611038;