rs11672983

Variant names:

• chr19-54871595-G-A
• rs11672983

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 0.349 in 152,048 control chromosomes in the GnomAD database, including 9,736 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 0.35 (9736 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.703
• Publications: 49 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.392 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: 0.349 AC: 52997 AN: 151930 Hom.: 9723 Cov.: 32

Gnomad AFR AF: 0.226

Gnomad AMI AF: 0.397

Gnomad AMR AF: 0.401

Gnomad ASJ AF: 0.477

Gnomad EAS AF: 0.284

Gnomad SAS AF: 0.406

Gnomad FIN AF: 0.427

Gnomad MID AF: 0.320

Gnomad NFE AF: 0.393

Gnomad OTH AF: 0.367

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

GnomAD4 genome AF: 0.349 AC: 53044 AN: 152048 Hom.: 9736 Cov.: 32 AF XY: 0.353 AC XY: 26265 AN XY: 74320

African (AFR) AF: 0.226 AC: 9372 AN: 41486

American (AMR) AF: 0.401 AC: 6123 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.477 AC: 1655 AN: 3470

East Asian (EAS) AF: 0.284 AC: 1471 AN: 5174

South Asian (SAS) AF: 0.407 AC: 1966 AN: 4830

European-Finnish (FIN) AF: 0.427 AC: 4499 AN: 10542

Middle Eastern (MID) AF: 0.320 AC: 94 AN: 294

European-Non Finnish (NFE) AF: 0.393 AC: 26715 AN: 67956

Other (OTH) AF: 0.374 AC: 789 AN: 2112

Alfa AF: 0.375 Hom.: 27249

Bravo AF: 0.339

Asia WGS AF: 0.394 AC: 1375 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.5
DANN	Benign	0.69
PhyloP100		0.70

Splicing

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

Other links and lift over

dbSNP: rs11672983; hg19: chr19-55383051;