rs7812088

Variant names:

• chr7-151222743-G-A
• rs7812088
• NM_007189.3:c.723-127C>T

Your query was ambiguous. Multiple possible variants found:

• chr7-151222743-G-A
• chr7-151222743-G-C

Variant summary

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

The NM_007189.3(ABCF2):​c.723-127C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.1 in 657,252 control chromosomes in the GnomAD database, including 3,848 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 (738 hom., cov: 32)
  • Exomes 𝑓: 0.10 (3110 hom.)
• Consequence: ABCF2 NM_007189.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.60
• Publications: 44 publications found

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:54751): (ABCF2-H2BK1 readthrough) This gene represents readthrough transcription between ABCF2 and a downstream histone H2B-like gene. [provided by RefSeq, Mar 2019]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.115 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_007189.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ABCF2	NM_007189.3	MANE Select	c.723-127C>T		intron	N/A	NP_009120.1
	ABCF2-H2BK1	NM_005692.5		c.723-127C>T		intron	N/A	NP_005683.2
	ABCF2-H2BK1	NR_160983.1		n.808-127C>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ABCF2	ENST00000287844.7	TSL:1 MANE Select	c.723-127C>T		intron	N/A	ENSP00000287844.2
	ABCF2-H2BK1	ENST00000222388.6	TSL:5	c.723-127C>T		intron	N/A	ENSP00000222388.2
	ABCF2	ENST00000468073.5	TSL:2	c.723-127C>T		intron	N/A	ENSP00000419720.1

Frequencies

GnomAD3 genomes AF: 0.0901 AC: 13692 AN: 152010 Hom.: 737 Cov.: 32

Gnomad AFR AF: 0.0568

Gnomad AMI AF: 0.0252

Gnomad AMR AF: 0.0631

Gnomad ASJ AF: 0.0956

Gnomad EAS AF: 0.000961

Gnomad SAS AF: 0.0878

Gnomad FIN AF: 0.136

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.117

Gnomad OTH AF: 0.0813

GnomAD4 exome AF: 0.103 AC: 52240 AN: 505124 Hom.: 3110 AF XY: 0.103 AC XY: 27462 AN XY: 266230

African (AFR) AF: 0.0583 AC: 770 AN: 13214

American (AMR) AF: 0.0501 AC: 1034 AN: 20652

Ashkenazi Jewish (ASJ) AF: 0.0997 AC: 1451 AN: 14548

East Asian (EAS) AF: 0.000199 AC: 6 AN: 30186

South Asian (SAS) AF: 0.0955 AC: 4409 AN: 46182

European-Finnish (FIN) AF: 0.141 AC: 4919 AN: 34844

Middle Eastern (MID) AF: 0.0788 AC: 282 AN: 3578

European-Non Finnish (NFE) AF: 0.117 AC: 36706 AN: 314732

Other (OTH) AF: 0.0979 AC: 2663 AN: 27188

GnomAD4 genome AF: 0.0900 AC: 13694 AN: 152128 Hom.: 738 Cov.: 32 AF XY: 0.0898 AC XY: 6676 AN XY: 74362

African (AFR) AF: 0.0567 AC: 2352 AN: 41476

American (AMR) AF: 0.0630 AC: 963 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.0956 AC: 332 AN: 3472

East Asian (EAS) AF: 0.000963 AC: 5 AN: 5192

South Asian (SAS) AF: 0.0883 AC: 425 AN: 4814

European-Finnish (FIN) AF: 0.136 AC: 1435 AN: 10588

Middle Eastern (MID) AF: 0.0714 AC: 21 AN: 294

European-Non Finnish (NFE) AF: 0.117 AC: 7968 AN: 67988

Other (OTH) AF: 0.0804 AC: 170 AN: 2114

Alfa AF: 0.107 Hom.: 2959

Bravo AF: 0.0822

Asia WGS AF: 0.0410 AC: 142 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	12
DANN	Benign	0.73
PhyloP100		1.6
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.050		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: rs7812088; hg19: chr7-150919829; COSMIC: COSV55182533; COSMIC: COSV55182533;