rs746698270

Variant names:

• chr16-2210005-C-A
• rs746698270
• NM_182563.4:c.383G>T

Your query was ambiguous. Multiple possible variants found:

• chr16-2210005-C-A
• chr16-2210005-C-G
• chr16-2210005-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_182563.4(BRICD5):​c.383G>T​(p.Arg128Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000071 in 1,408,138 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R128H) has been classified as Uncertain significance.

• Frequency:
  • Genomes: not found (cov: 34)
  • Exomes 𝑓: 7.1e-7 (0 hom.)
• Consequence: BRICD5 NM_182563.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.08

Genes affected

BRICD5 (HGNC:28309): (BRICHOS domain containing 5) Predicted to be involved in regulation of cell population proliferation. Predicted to be integral component of membrane. Predicted to be active in extracellular space. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.13616678).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BRICD5	NM_182563.4	c.383G>T	p.Arg128Leu	missense_variant	Exon 4 of 6	ENST00000328540.8	NP_872369.2
BRICD5	XM_047433958.1	c.383G>T	p.Arg128Leu	missense_variant	Exon 4 of 5		XP_047289914.1
BRICD5	XM_047433959.1	c.449G>T	p.Arg150Leu	missense_variant	Exon 2 of 4		XP_047289915.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BRICD5	ENST00000328540.8	c.383G>T	p.Arg128Leu	missense_variant	Exon 4 of 6	1	NM_182563.4	ENSP00000332389.3
BRICD5	ENST00000562360.5	c.383G>T	p.Arg128Leu	missense_variant	Exon 4 of 5	2		ENSP00000455052.1
BRICD5	ENST00000566018.1	c.457G>T	p.Ala153Ser	missense_variant	Exon 3 of 3	2		ENSP00000457969.1
BRICD5	ENST00000566795.1	n.141G>T		non_coding_transcript_exon_variant	Exon 1 of 2	3

Frequencies

GnomAD3 genomes Cov.: 34

GnomAD4 exome AF: 7.10e-7 AC: 1 AN: 1408138 Hom.: 0 Cov.: 33 AF XY: 0.00000144 AC XY: 1 AN XY: 693020

Gnomad4 AFR exome AF: 0.0000307

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 34

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Uncertain	0.42
BayesDel_addAF	Benign	-0.20	T
BayesDel_noAF	Benign	-0.18
CADD	Benign	19
DANN	Uncertain	1.0
Eigen	Benign	-0.081
Eigen_PC	Benign	-0.15
FATHMM_MKL	Benign	0.42	N
LIST_S2	Benign	0.24	T
M_CAP	Uncertain	0.17	D
MetaRNN	Benign	0.14	T
PROVEAN	Benign	0.31	N
Sift	Pathogenic	0.0	D
Vest4		0.20
MVP		0.34
ClinPred		0.96	D
GERP RS		2.5
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		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: rs746698270; hg19: chr16-2260006;