rs7161377

Variant names:

• chr14-75535051-T-C
• rs7161377
• NM_006399.5:c.168+9863T>C

Variant summary

Our verdict is Benign. Variant got -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

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=-0.85).
• 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

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

Gnomad4 AFR AF: 0.472

Gnomad4 AMR AF: 0.560

Gnomad4 ASJ AF: 0.556

Gnomad4 EAS AF: 0.612

Gnomad4 SAS AF: 0.646

Gnomad4 FIN AF: 0.655

Gnomad4 NFE AF: 0.526

Gnomad4 OTH AF: 0.491

Alfa AF: 0.534 Hom.: 3681

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

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: rs7161377; hg19: chr14-76001394;