rs1156058

Positions:

• chr1-212696194-C-A
• chr1-212696194-C-T

Variant summary

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

The NM_018664.3(BATF3):​c.195+767G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.628 in 151,654 control chromosomes in the GnomAD database, including 30,299 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 0.63 (30299 hom., cov: 30)
• Consequence: BATF3 NM_018664.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.644

Genes affected

BATF3 (HGNC:28915): (basic leucine zipper ATF-like transcription factor 3) This gene encodes a member of the basic leucine zipper protein family. The encoded protein functions as a transcriptional repressor when heterodimerizing with JUN. The protein may play a role in repression of interleukin-2 and matrix metalloproteinase-1 transcription.[provided by RefSeq, Feb 2009]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.655 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BATF3	NM_018664.3	c.195+767G>T		intron_variant		ENST00000243440.2	NP_061134.1
BATF3	XR_001737289.2	n.273+767G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BATF3	ENST00000243440.2	c.195+767G>T		intron_variant		1	NM_018664.3	ENSP00000243440	P1
BATF3	ENST00000478275.1	n.1795+767G>T		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.628 AC: 95210 AN: 151560 Hom.: 30274 Cov.: 30

Gnomad AFR AF: 0.609

Gnomad AMI AF: 0.598

Gnomad AMR AF: 0.470

Gnomad ASJ AF: 0.609

Gnomad EAS AF: 0.642

Gnomad SAS AF: 0.670

Gnomad FIN AF: 0.713

Gnomad MID AF: 0.674

Gnomad NFE AF: 0.660

Gnomad OTH AF: 0.613

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

GnomAD4 genome AF: 0.628 AC: 95260 AN: 151654 Hom.: 30299 Cov.: 30 AF XY: 0.630 AC XY: 46635 AN XY: 74082

Gnomad4 AFR AF: 0.609

Gnomad4 AMR AF: 0.469

Gnomad4 ASJ AF: 0.609

Gnomad4 EAS AF: 0.642

Gnomad4 SAS AF: 0.670

Gnomad4 FIN AF: 0.713

Gnomad4 NFE AF: 0.660

Gnomad4 OTH AF: 0.608

Alfa AF: 0.651 Hom.: 8758

Bravo AF: 0.603

Asia WGS AF: 0.588 AC: 2046 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	5.7
DANN	Benign	0.63

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: rs1156058; hg19: chr1-212869536;