rs1378335

Variant names:

• chr11-102241446-C-G
• rs1378335

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;