rs1122979

Positions:

• chr7-151217985-G-A

Variant summary

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

The NM_007189.3(ABCF2):​c.1338+96C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.102 in 884,042 control chromosomes in the GnomAD database, including 5,284 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 0.090 (733 hom., cov: 31)
  • Exomes 𝑓: 0.10 (4551 hom.)
• Consequence: ABCF2 NM_007189.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.342

Genes affected

ABCF2 (HGNC:71): (ATP binding cassette subfamily F member 2) This gene encodes a member of the ATP-binding cassette (ABC) transporter superfamily. ATP-binding cassette proteins transport various molecules across extra- and intracellular membranes. Alterations in this gene may be involved in cancer progression. Related pseudogenes have been identified on chromosomes 3 and 7. [provided by RefSeq, Mar 2019]

ABCF2-H2BK1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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 = 0.115 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ABCF2	NM_007189.3	c.1338+96C>T		intron_variant		ENST00000287844.7
ABCF2-H2BK1	NR_160983.1	n.1423+96C>T		intron_variant, non_coding_transcript_variant
ABCF2-H2BK1	NM_005692.5	c.1338+96C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ABCF2	ENST00000287844.7	c.1338+96C>T		intron_variant		1	NM_007189.3	P1

Frequencies

GnomAD3 genomes AF: 0.0900 AC: 13663 AN: 151748 Hom.: 732 Cov.: 31

Gnomad AFR AF: 0.0567

Gnomad AMI AF: 0.0252

Gnomad AMR AF: 0.0635

Gnomad ASJ AF: 0.0956

Gnomad EAS AF: 0.000964

Gnomad SAS AF: 0.0881

Gnomad FIN AF: 0.135

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.117

Gnomad OTH AF: 0.0815

GnomAD4 exome AF: 0.104 AC: 76385 AN: 732176 Hom.: 4551 AF XY: 0.104 AC XY: 39614 AN XY: 380206

Gnomad4 AFR exome AF: 0.0550

Gnomad4 AMR exome AF: 0.0447

Gnomad4 ASJ exome AF: 0.101

Gnomad4 EAS exome AF: 0.000196

Gnomad4 SAS exome AF: 0.0949

Gnomad4 FIN exome AF: 0.142

Gnomad4 NFE exome AF: 0.116

Gnomad4 OTH exome AF: 0.0981

GnomAD4 genome AF: 0.0900 AC: 13665 AN: 151866 Hom.: 733 Cov.: 31 AF XY: 0.0898 AC XY: 6662 AN XY: 74206

Gnomad4 AFR AF: 0.0566

Gnomad4 AMR AF: 0.0634

Gnomad4 ASJ AF: 0.0956

Gnomad4 EAS AF: 0.000966

Gnomad4 SAS AF: 0.0886

Gnomad4 FIN AF: 0.135

Gnomad4 NFE AF: 0.117

Gnomad4 OTH AF: 0.0806

Alfa AF: 0.109 Hom.: 295

Bravo AF: 0.0822

Asia WGS AF: 0.0410 AC: 143 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	3.3
DANN	Benign	0.36

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: rs1122979; hg19: chr7-150915071; COSMIC: COSV55182528; COSMIC: COSV55182528;