rs11880865

Variant names:

• chr19-10960472-A-T
• rs11880865

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 0.37 in 152,052 control chromosomes in the GnomAD database, including 10,466 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 0.37 (10466 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.30
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.451 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: 0.370 AC: 56182 AN: 151934 Hom.: 10445 Cov.: 33

Gnomad AFR AF: 0.368

Gnomad AMI AF: 0.320

Gnomad AMR AF: 0.313

Gnomad ASJ AF: 0.376

Gnomad EAS AF: 0.266

Gnomad SAS AF: 0.466

Gnomad FIN AF: 0.357

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.387

Gnomad OTH AF: 0.368

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

GnomAD4 genome AF: 0.370 AC: 56250 AN: 152052 Hom.: 10466 Cov.: 33 AF XY: 0.369 AC XY: 27462 AN XY: 74332

African (AFR) AF: 0.369 AC: 15291 AN: 41494

American (AMR) AF: 0.313 AC: 4778 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.376 AC: 1305 AN: 3472

East Asian (EAS) AF: 0.267 AC: 1381 AN: 5174

South Asian (SAS) AF: 0.467 AC: 2251 AN: 4820

European-Finnish (FIN) AF: 0.357 AC: 3770 AN: 10574

Middle Eastern (MID) AF: 0.463 AC: 136 AN: 294

European-Non Finnish (NFE) AF: 0.387 AC: 26269 AN: 67934

Other (OTH) AF: 0.369 AC: 777 AN: 2106

Alfa AF: 0.369 Hom.: 1351

Bravo AF: 0.364

Asia WGS AF: 0.385 AC: 1339 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.17
DANN	Benign	0.50
PhyloP100		-1.3
PromoterAI		-0.073	Neutral

Splicing

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

Other links and lift over

dbSNP: rs11880865; hg19: chr19-11071148;