14-75539214-T-C

Position:

• chr14-75539214-T-C

Variant summary

Our verdict is Benign. Variant got -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

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]

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BATF	NM_006399.5	c.169-7248T>C		intron_variant		ENST00000286639.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BATF	ENST00000286639.8	c.169-7248T>C		intron_variant		1	NM_006399.5	P1
BATF	ENST00000555504.1	c.151-7692T>C		intron_variant		2
BATF	ENST00000555795.1	n.192-7248T>C		intron_variant, non_coding_transcript_variant		3

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

Gnomad4 AFR AF: 0.0883

Gnomad4 AMR AF: 0.227

Gnomad4 ASJ AF: 0.229

Gnomad4 EAS AF: 0.290

Gnomad4 SAS AF: 0.273

Gnomad4 FIN AF: 0.202

Gnomad4 NFE AF: 0.254

Gnomad4 OTH AF: 0.245

Alfa AF: 0.247 Hom.: 10755

Bravo AF: 0.202

Asia WGS AF: 0.246 AC: 861 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.7
DANN	Benign	0.39

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: rs2300603; hg19: chr14-76005557;