rs17783132

chr14-75523780-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_006399.5(BATF):c.63+1035G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0855 in 152,206 control chromosomes in the GnomAD database, including 703 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 0.086 (703 hom., cov: 31)
• Consequence: BATF NM_006399.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.412

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=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.124 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BATF	NM_006399.5	c.63+1035G>A		intron_variant		ENST00000286639.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BATF	ENST00000286639.8	c.63+1035G>A		intron_variant		1	NM_006399.5	P1
BATF	ENST00000555504.1	c.63+1035G>A		intron_variant		2
BATF	ENST00000555795.1	n.86+1240G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.0856 AC: 13025 AN: 152088 Hom.: 705 Cov.: 31

Gnomad AFR AF: 0.0313

Gnomad AMI AF: 0.144

Gnomad AMR AF: 0.0845

Gnomad ASJ AF: 0.122

Gnomad EAS AF: 0.000577

Gnomad SAS AF: 0.0220

Gnomad FIN AF: 0.0892

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.126

Gnomad OTH AF: 0.102

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

GnomAD4 genome AF: 0.0855 AC: 13017 AN: 152206 Hom.: 703 Cov.: 31 AF XY: 0.0818 AC XY: 6087 AN XY: 74396

Gnomad4 AFR AF: 0.0313

Gnomad4 AMR AF: 0.0841

Gnomad4 ASJ AF: 0.122

Gnomad4 EAS AF: 0.000579

Gnomad4 SAS AF: 0.0214

Gnomad4 FIN AF: 0.0892

Gnomad4 NFE AF: 0.126

Gnomad4 OTH AF: 0.101

Alfa AF: 0.0992 Hom.: 142

Bravo AF: 0.0860

Asia WGS AF: 0.0200 AC: 71 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.72
Dann	Benign	0.58

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: rs17783132; hg19: chr14-75990123;