chr14-75535051-T-C

Variant names:

• chr14-75535051-T-C
• rs7161377
• NM_006399.5:c.168+9863T>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.168+9863T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.529 in 152,064 control chromosomes in the GnomAD database, including 21,461 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 0.53 (21461 hom., cov: 32)
• Consequence: BATF NM_006399.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.349
• Publications: 3 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=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.627 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BATF	NM_006399.5	c.168+9863T>C		intron_variant	Intron 2 of 2	ENST00000286639.8	NP_006390.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BATF	ENST00000286639.8	c.168+9863T>C		intron_variant	Intron 2 of 2	1	NM_006399.5	ENSP00000286639.6
BATF	ENST00000555504.1	c.150+9881T>C		intron_variant	Intron 2 of 2	2		ENSP00000450486.1
BATF	ENST00000555795.1	n.191+9863T>C		intron_variant	Intron 2 of 2	3
ENSG00000297883	ENST00000751543.1	n.73+15735A>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.529 AC: 80455 AN: 151946 Hom.: 21450 Cov.: 32

Gnomad AFR AF: 0.473

Gnomad AMI AF: 0.300

Gnomad AMR AF: 0.559

Gnomad ASJ AF: 0.556

Gnomad EAS AF: 0.612

Gnomad SAS AF: 0.645

Gnomad FIN AF: 0.655

Gnomad MID AF: 0.528

Gnomad NFE AF: 0.526

Gnomad OTH AF: 0.489

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

GnomAD4 genome AF: 0.529 AC: 80489 AN: 152064 Hom.: 21461 Cov.: 32 AF XY: 0.539 AC XY: 40038 AN XY: 74342

African (AFR) AF: 0.472 AC: 19587 AN: 41470

American (AMR) AF: 0.560 AC: 8558 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.556 AC: 1928 AN: 3470

East Asian (EAS) AF: 0.612 AC: 3169 AN: 5180

South Asian (SAS) AF: 0.646 AC: 3117 AN: 4828

European-Finnish (FIN) AF: 0.655 AC: 6919 AN: 10562

Middle Eastern (MID) AF: 0.534 AC: 157 AN: 294

European-Non Finnish (NFE) AF: 0.526 AC: 35745 AN: 67954

Other (OTH) AF: 0.491 AC: 1035 AN: 2110

Alfa AF: 0.533 Hom.: 3763

Bravo AF: 0.513

Asia WGS AF: 0.633 AC: 2197 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	0.92
DANN	Benign	0.88
PhyloP100		-0.35
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: rs7161377; hg19: chr14-76001394;