rs17783132

Variant names:

• chr14-75523780-G-A
• rs17783132
• NM_006399.5:c.63+1035G>A

Variant summary

Our verdict is Benign. The variant received -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
• 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=-0.9).
• 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 rank	MANE	Protein	UniProt
BATF	NM_006399.5	c.63+1035G>A		intron_variant	Intron 1 of 2	ENST00000286639.8	NP_006390.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BATF	ENST00000286639.8	c.63+1035G>A		intron_variant	Intron 1 of 2	1	NM_006399.5	ENSP00000286639.6
BATF	ENST00000555504.1	c.63+1035G>A		intron_variant	Intron 1 of 2	2		ENSP00000450486.1
BATF	ENST00000555795.1	n.86+1240G>A		intron_variant	Intron 1 of 2	3
ENSG00000297883	ENST00000751543.1	n.74-25366C>T		intron_variant	Intron 1 of 2

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

African (AFR) AF: 0.0313 AC: 1298 AN: 41532

American (AMR) AF: 0.0841 AC: 1286 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.122 AC: 422 AN: 3472

East Asian (EAS) AF: 0.000579 AC: 3 AN: 5184

South Asian (SAS) AF: 0.0214 AC: 103 AN: 4814

European-Finnish (FIN) AF: 0.0892 AC: 944 AN: 10584

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.126 AC: 8589 AN: 68012

Other (OTH) AF: 0.101 AC: 213 AN: 2110

Alfa AF: 0.0972 Hom.: 144

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
PhyloP100		-0.41
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: rs17783132; hg19: chr14-75990123;