rs11861379

Positions:

• chr16-48234407-T-C

Variant summary

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

The NM_001370497.1(ABCC11):​c.-18-2468A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.131 in 152,218 control chromosomes in the GnomAD database, including 1,621 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 0.13 (1621 hom., cov: 33)
• Consequence: ABCC11 NM_001370497.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.781

Genes affected

ABCC11 (HGNC:14639): (ATP binding cassette subfamily C member 11) 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, White). This ABC full transporter is a member of the MRP subfamily which is involved in multi-drug resistance. The product of this gene participates in physiological processes involving bile acids, conjugated steroids, and cyclic nucleotides. In addition, a SNP in this gene is responsible for determination of human earwax type. This gene and family member ABCC12 are determined to be derived by duplication and are both localized to chromosome 16q12.1. Multiple alternatively spliced transcript variants have been described for this gene. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.231 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ABCC11	NM_001370497.1	c.-18-2468A>G		intron_variant		ENST00000356608.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ABCC11	ENST00000356608.7	c.-18-2468A>G		intron_variant		1	NM_001370497.1	P1

Frequencies

GnomAD3 genomes AF: 0.131 AC: 19880 AN: 152100 Hom.: 1612 Cov.: 33

Gnomad AFR AF: 0.234

Gnomad AMI AF: 0.0603

Gnomad AMR AF: 0.0982

Gnomad ASJ AF: 0.0997

Gnomad EAS AF: 0.0152

Gnomad SAS AF: 0.0543

Gnomad FIN AF: 0.115

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.0948

Gnomad OTH AF: 0.117

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

GnomAD4 genome AF: 0.131 AC: 19918 AN: 152218 Hom.: 1621 Cov.: 33 AF XY: 0.130 AC XY: 9665 AN XY: 74444

Gnomad4 AFR AF: 0.234

Gnomad4 AMR AF: 0.0979

Gnomad4 ASJ AF: 0.0997

Gnomad4 EAS AF: 0.0154

Gnomad4 SAS AF: 0.0535

Gnomad4 FIN AF: 0.115

Gnomad4 NFE AF: 0.0948

Gnomad4 OTH AF: 0.117

Alfa AF: 0.101 Hom.: 1153

Bravo AF: 0.132

Asia WGS AF: 0.0640 AC: 224 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	6.9
DANN	Benign	0.28

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: rs11861379; hg19: chr16-48268318;