chr5-126402275-A-C

Variant names:

• chr5-126402275-A-C
• rs4836255
• NM_001146319.3:c.128+41816A>C

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001146319.3(GRAMD2B):​c.128+41816A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
• Consequence: GRAMD2B NM_001146319.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.503
• Publications: 3 publications found

Genes affected

GRAMD2B (HGNC:24911): (GRAM domain containing 2B) Enables identical protein binding activity. Located in cytoplasmic microtubule. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000250602 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GRAMD2B	NM_001146319.3	c.128+41816A>C		intron_variant	Intron 1 of 13		NP_001139791.1
GRAMD2B	XM_011543593.3	c.128+41816A>C		intron_variant	Intron 1 of 13		XP_011541895.1
GRAMD2B	XM_005272057.5	c.125+30708A>C		intron_variant	Intron 1 of 13		XP_005272114.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GRAMD2B	ENST00000513040.5	c.128+41816A>C		intron_variant	Intron 1 of 13	2		ENSP00000426120.1
GRAMD2B	ENST00000506445.5	c.125+30708A>C		intron_variant	Intron 1 of 8	5		ENSP00000424985.1
ENSG00000250602	ENST00000648070.1	n.896-8645T>G		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.4
DANN	Benign	0.85
PhyloP100		-0.50

Splicing

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

Other links and lift over

dbSNP: rs4836255; hg19: chr5-125737967;