rs1378335

Positions:

• chr11-102241446-C-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 0.928 in 152,242 control chromosomes in the GnomAD database, including 65,685 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 0.93 (65685 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.108

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.967 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: 0.928 AC: 141118 AN: 152124 Hom.: 65618 Cov.: 31

Gnomad AFR AF: 0.975

Gnomad AMI AF: 0.919

Gnomad AMR AF: 0.956

Gnomad ASJ AF: 0.877

Gnomad EAS AF: 0.784

Gnomad SAS AF: 0.808

Gnomad FIN AF: 0.933

Gnomad MID AF: 0.915

Gnomad NFE AF: 0.914

Gnomad OTH AF: 0.933

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

GnomAD4 genome AF: 0.928 AC: 141247 AN: 152242 Hom.: 65685 Cov.: 31 AF XY: 0.926 AC XY: 68886 AN XY: 74416

Gnomad4 AFR AF: 0.975

Gnomad4 AMR AF: 0.956

Gnomad4 ASJ AF: 0.877

Gnomad4 EAS AF: 0.784

Gnomad4 SAS AF: 0.809

Gnomad4 FIN AF: 0.933

Gnomad4 NFE AF: 0.914

Gnomad4 OTH AF: 0.933

Alfa AF: 0.920 Hom.: 8010

Bravo AF: 0.933

Asia WGS AF: 0.823 AC: 2861 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.0
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1378335; hg19: chr11-102112177;