14-75539214-T-C

Variant names:

• chr14-75539214-T-C
• rs2300603
• NM_006399.5:c.169-7248T>C

Variant summary

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

The NM_006399.5(BATF):​c.169-7248T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.205 in 152,148 control chromosomes in the GnomAD database, including 3,657 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 0.20 (3657 hom., cov: 31)
• Consequence: BATF NM_006399.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.193
• Publications: 43 publications found

Genes affected

BATF (HGNC:958): (basic leucine zipper ATF-like transcription factor) The protein encoded by this gene is a nuclear basic leucine zipper protein that belongs to the AP-1/ATF superfamily of transcription factors. The leucine zipper of this protein mediates dimerization with members of the Jun family of proteins. This protein is thought to be a negative regulator of AP-1/ATF transcriptional events. [provided by RefSeq, Jul 2008]

ENSG00000297883 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.278 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_006399.5. 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
	BATF	NM_006399.5	MANE Select	c.169-7248T>C		intron	N/A	NP_006390.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BATF	ENST00000286639.8	TSL:1 MANE Select	c.169-7248T>C		intron	N/A	ENSP00000286639.6
	BATF	ENST00000555504.1	TSL:2	c.151-7692T>C		intron	N/A	ENSP00000450486.1
	BATF	ENST00000555795.1	TSL:3	n.192-7248T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.205 AC: 31148 AN: 152030 Hom.: 3657 Cov.: 31

Gnomad AFR AF: 0.0882

Gnomad AMI AF: 0.475

Gnomad AMR AF: 0.227

Gnomad ASJ AF: 0.229

Gnomad EAS AF: 0.291

Gnomad SAS AF: 0.273

Gnomad FIN AF: 0.202

Gnomad MID AF: 0.287

Gnomad NFE AF: 0.254

Gnomad OTH AF: 0.245

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

GnomAD4 genome AF: 0.205 AC: 31153 AN: 152148 Hom.: 3657 Cov.: 31 AF XY: 0.205 AC XY: 15241 AN XY: 74384

African (AFR) AF: 0.0883 AC: 3668 AN: 41544

American (AMR) AF: 0.227 AC: 3466 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.229 AC: 793 AN: 3470

East Asian (EAS) AF: 0.290 AC: 1501 AN: 5174

South Asian (SAS) AF: 0.273 AC: 1314 AN: 4814

European-Finnish (FIN) AF: 0.202 AC: 2133 AN: 10566

Middle Eastern (MID) AF: 0.284 AC: 83 AN: 292

European-Non Finnish (NFE) AF: 0.254 AC: 17246 AN: 67986

Other (OTH) AF: 0.245 AC: 517 AN: 2110

Alfa AF: 0.240 Hom.: 21377

Bravo AF: 0.202

Asia WGS AF: 0.246 AC: 861 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.7
DANN	Benign	0.39
PhyloP100		-0.19
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: rs2300603; hg19: chr14-76005557;