rs7215642

Variant names:

• chr17-69031729-A-G
• rs7215642
• NM_080283.4:c.1445+379T>C

Your query was ambiguous. Multiple possible variants found:

• chr17-69031729-A-G
• chr17-69031729-A-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_080283.4(ABCA9):​c.1445+379T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.592 in 151,984 control chromosomes in the GnomAD database, including 27,801 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 0.59 (27801 hom., cov: 31)
• Consequence: ABCA9 NM_080283.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.36
• Publications: 5 publications found

Genes affected

ABCA9 (HGNC:39): (ATP binding cassette subfamily A member 9) This gene is a member of the superfamily of ATP-binding cassette (ABC) transporters and the encoded protein contains two transmembrane domains and two nucleotide binding folds. ABC proteins transport various molecules across extra- and intracellular membranes. ABC genes are divided into seven distinct subfamilies (ABC1, MDR/TAP, MRP, ALD, OABP, GCN20, and White). This gene is a member of the ABC1 subfamily and is clustered with four other ABC1 family members on chromosome 17q24. Transcriptional expression of this gene is induced during monocyte differentiation into macrophages and is suppressed by cholesterol import. [provided by RefSeq, Jul 2008]

ABCA9-AS1 (HGNC:39983): (ABCA9 antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.685 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ABCA9	NM_080283.4	c.1445+379T>C		intron_variant	Intron 10 of 38	ENST00000340001.9	NP_525022.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ABCA9	ENST00000340001.9	c.1445+379T>C		intron_variant	Intron 10 of 38	1	NM_080283.4	ENSP00000342216.3
ABCA9	ENST00000453985.6	c.1445+379T>C		intron_variant	Intron 10 of 37	5		ENSP00000394264.2
ABCA9-AS1	ENST00000627453.2	n.238-892A>G		intron_variant	Intron 4 of 5	5
ABCA9-AS1	ENST00000629311.1	n.230-892A>G		intron_variant	Intron 3 of 4	5

Frequencies

GnomAD3 genomes AF: 0.592 AC: 89943 AN: 151866 Hom.: 27787 Cov.: 31

Gnomad AFR AF: 0.428

Gnomad AMI AF: 0.733

Gnomad AMR AF: 0.616

Gnomad ASJ AF: 0.689

Gnomad EAS AF: 0.335

Gnomad SAS AF: 0.608

Gnomad FIN AF: 0.641

Gnomad MID AF: 0.725

Gnomad NFE AF: 0.690

Gnomad OTH AF: 0.595

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

GnomAD4 genome AF: 0.592 AC: 89998 AN: 151984 Hom.: 27801 Cov.: 31 AF XY: 0.589 AC XY: 43783 AN XY: 74274

African (AFR) AF: 0.428 AC: 17735 AN: 41436

American (AMR) AF: 0.615 AC: 9393 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.689 AC: 2388 AN: 3464

East Asian (EAS) AF: 0.336 AC: 1736 AN: 5168

South Asian (SAS) AF: 0.607 AC: 2925 AN: 4816

European-Finnish (FIN) AF: 0.641 AC: 6757 AN: 10548

Middle Eastern (MID) AF: 0.731 AC: 215 AN: 294

European-Non Finnish (NFE) AF: 0.690 AC: 46929 AN: 67972

Other (OTH) AF: 0.595 AC: 1254 AN: 2106

Alfa AF: 0.667 Hom.: 21845

Bravo AF: 0.578

Asia WGS AF: 0.506 AC: 1761 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	11
DANN	Benign	0.62
PhyloP100		1.4
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs7215642; hg19: chr17-67027870;