rs752459864

Variant names:

• chr6-43432764-G-A
• rs752459864
• NM_001198934.2:c.784G>A

Your query was ambiguous. Multiple possible variants found:

• chr6-43432764-G-A
• chr6-43432764-G-T

Variant summary

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

The NM_001198934.2(ABCC10):​c.784G>A​(p.Val262Ile) variant causes a missense 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. 16/21 in silico tools predict 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. V262F) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 33)
• Consequence: ABCC10 NM_001198934.2 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.288

Genes affected

ABCC10 (HGNC:52): (ATP binding cassette subfamily C member 10) The protein encoded by this gene is a member of the superfamily of ATP-binding cassette (ABC) transporters. ABC proteins transport various molecules across extra- and intra-cellular membranes. ABC genes are divided into seven distinct subfamilies (ABC1, MDR/TAP, MRP, ALD, OABP, GCN20, and White). This ABC full-transporter is a member of the MRP subfamily which is involved in multi-drug resistance. Multiple transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Nov 2010]

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=0.0804334).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ABCC10	NM_001198934.2	c.784G>A	p.Val262Ile	missense_variant	Exon 3 of 22	ENST00000372530.9	NP_001185863.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ABCC10	ENST00000372530.9	c.784G>A	p.Val262Ile	missense_variant	Exon 3 of 22	2	NM_001198934.2	ENSP00000361608.4
ABCC10	ENST00000244533.7	c.655G>A	p.Val219Ile	missense_variant	Exon 1 of 20	1		ENSP00000244533.3
ABCC10	ENST00000372515.8	c.-78-471G>A		intron_variant	Intron 1 of 7	5		ENSP00000361593.4
ABCC10	ENST00000443426.2	n.113-471G>A		intron_variant	Intron 1 of 2	2

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 84

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.076
BayesDel_addAF	Benign	-0.15	T
BayesDel_noAF	Benign	-0.45
CADD	Benign	0.98
DANN	Benign	0.92
DEOGEN2	Benign	0.044	T;.
Eigen	Benign	-1.0
Eigen_PC	Benign	-1.0
FATHMM_MKL	Benign	0.20	N
LIST_S2	Benign	0.60	T;T
M_CAP	Benign	0.018	T
MetaRNN	Benign	0.080	T;T
MetaSVM	Benign	-0.82	T
MutationAssessor	Benign	0.0	N;.
PrimateAI	Benign	0.41	T
PROVEAN	Benign	-0.47	N;N
REVEL	Benign	0.13
Sift	Benign	0.44	T;T
Sift4G	Benign	0.39	T;T
Polyphen		0.0	B;B
Vest4		0.067
MutPred		0.36		Loss of MoRF binding (P = 0.1263);.;
MVP		0.34
MPC		0.13
ClinPred		0.027	T
GERP RS		-0.084
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7
Varity_R		0.030
gMVP		0.086

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs752459864; hg19: chr6-43400502;