rs1378736

chr11-5044857-A-G

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 0.512 in 151,868 control chromosomes in the GnomAD database, including 20,182 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 0.51 (20182 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.17

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.56 is higher than 0.05.

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: 0.512 AC: 77658 AN: 151752 Hom.: 20148 Cov.: 31

Gnomad AFR AF: 0.567

Gnomad AMI AF: 0.548

Gnomad AMR AF: 0.522

Gnomad ASJ AF: 0.546

Gnomad EAS AF: 0.263

Gnomad SAS AF: 0.524

Gnomad FIN AF: 0.480

Gnomad MID AF: 0.627

Gnomad NFE AF: 0.496

Gnomad OTH AF: 0.525

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

GnomAD4 genome AF: 0.512 AC: 77733 AN: 151868 Hom.: 20182 Cov.: 31 AF XY: 0.510 AC XY: 37825 AN XY: 74232

Gnomad4 AFR AF: 0.567

Gnomad4 AMR AF: 0.522

Gnomad4 ASJ AF: 0.546

Gnomad4 EAS AF: 0.262

Gnomad4 SAS AF: 0.526

Gnomad4 FIN AF: 0.480

Gnomad4 NFE AF: 0.496

Gnomad4 OTH AF: 0.528

Alfa AF: 0.506 Hom.: 25623

Bravo AF: 0.520

Asia WGS AF: 0.414 AC: 1438 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
Cadd	Benign	15
Dann	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1378736; hg19: chr11-5066087;