rs1029278

chr11-123550694-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001387025.1(GRAMD1B):c.453-26673A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.735 in 152,072 control chromosomes in the GnomAD database, including 41,843 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 0.73 (41843 hom., cov: 31)
• Consequence: GRAMD1B NM_001387025.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.707

Genes affected

GRAMD1B (HGNC:29214): (GRAM domain containing 1B) Predicted to enable cholesterol binding activity; cholesterol transfer activity; and phospholipid binding activity. Predicted to be involved in cellular response to cholesterol and cholesterol homeostasis. Located in endoplasmic reticulum membrane; endoplasmic reticulum-plasma membrane contact site; and plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.872 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GRAMD1B	NM_001387025.1	c.453-26673A>G		intron_variant		ENST00000635736.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GRAMD1B	ENST00000635736.2	c.453-26673A>G		intron_variant		5	NM_001387025.1	P1

Frequencies

GnomAD3 genomes AF: 0.735 AC: 111644 AN: 151954 Hom.: 41785 Cov.: 31

Gnomad AFR AF: 0.879

Gnomad AMI AF: 0.670

Gnomad AMR AF: 0.760

Gnomad ASJ AF: 0.652

Gnomad EAS AF: 0.682

Gnomad SAS AF: 0.515

Gnomad FIN AF: 0.735

Gnomad MID AF: 0.623

Gnomad NFE AF: 0.666

Gnomad OTH AF: 0.731

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

GnomAD4 genome AF: 0.735 AC: 111768 AN: 152072 Hom.: 41843 Cov.: 31 AF XY: 0.736 AC XY: 54730 AN XY: 74318

Gnomad4 AFR AF: 0.879

Gnomad4 AMR AF: 0.760

Gnomad4 ASJ AF: 0.652

Gnomad4 EAS AF: 0.681

Gnomad4 SAS AF: 0.516

Gnomad4 FIN AF: 0.735

Gnomad4 NFE AF: 0.666

Gnomad4 OTH AF: 0.733

Alfa AF: 0.685 Hom.: 48813

Bravo AF: 0.747

Asia WGS AF: 0.598 AC: 2079 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
Cadd	Benign	6.9
Dann	Benign	0.58

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs1029278; hg19: chr11-123421402;