chr7-151217985-G-A

Variant names:

• chr7-151217985-G-A
• rs1122979
• NM_007189.3:c.1338+96C>T

Variant summary

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

The NM_005692.5(ABCF2-H2BK1):​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-H2BK1 NM_005692.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.342
• Publications: 18 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=-0.85).
• 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_005692.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ABCF2	NM_007189.3	MANE Select	c.1338+96C>T		intron	N/A	NP_009120.1
	ABCF2-H2BK1	NM_005692.5		c.1338+96C>T		intron	N/A	NP_005683.2
	ABCF2-H2BK1	NR_160983.1		n.1423+96C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ABCF2	ENST00000287844.7	TSL:1 MANE Select	c.1338+96C>T		intron	N/A	ENSP00000287844.2
	ABCF2-H2BK1	ENST00000222388.6	TSL:5	c.1338+96C>T		intron	N/A	ENSP00000222388.2
	ABCF2	ENST00000889553.1		c.1338+96C>T		intron	N/A	ENSP00000559612.1

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

African (AFR) AF: 0.0550 AC: 1026 AN: 18662

American (AMR) AF: 0.0447 AC: 1428 AN: 31978

Ashkenazi Jewish (ASJ) AF: 0.101 AC: 1695 AN: 16820

East Asian (EAS) AF: 0.000196 AC: 7 AN: 35782

South Asian (SAS) AF: 0.0949 AC: 5625 AN: 59244

European-Finnish (FIN) AF: 0.142 AC: 6758 AN: 47744

Middle Eastern (MID) AF: 0.0773 AC: 320 AN: 4140

European-Non Finnish (NFE) AF: 0.116 AC: 56036 AN: 482232

Other (OTH) AF: 0.0981 AC: 3490 AN: 35574

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

African (AFR) AF: 0.0566 AC: 2341 AN: 41378

American (AMR) AF: 0.0634 AC: 968 AN: 15276

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

East Asian (EAS) AF: 0.000966 AC: 5 AN: 5174

South Asian (SAS) AF: 0.0886 AC: 426 AN: 4806

European-Finnish (FIN) AF: 0.135 AC: 1418 AN: 10508

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

European-Non Finnish (NFE) AF: 0.117 AC: 7961 AN: 67938

Other (OTH) AF: 0.0806 AC: 170 AN: 2108

Alfa AF: 0.105 Hom.: 309

Bravo AF: 0.0822

Asia WGS AF: 0.0410 AC: 143 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	3.3
DANN	Benign	0.36
PhyloP100		0.34
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: rs1122979; hg19: chr7-150915071; COSMIC: COSV55182528; COSMIC: COSV55182528;