rs1157907

chr2-14864624-T-C

Variant summary

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

The ENST00000654007.1(ENSG00000287291):n.856+122040A>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.291 in 152,000 control chromosomes in the GnomAD database, including 7,083 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 0.29 (7083 hom., cov: 31)
• Consequence: ENST00000654007.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.87

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.388 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NBAS	XR_007076390.1	n.7016-85477A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000654007.1	n.856+122040A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.291 AC: 44231 AN: 151880 Hom.: 7078 Cov.: 31

Gnomad AFR AF: 0.161

Gnomad AMI AF: 0.291

Gnomad AMR AF: 0.313

Gnomad ASJ AF: 0.293

Gnomad EAS AF: 0.403

Gnomad SAS AF: 0.363

Gnomad FIN AF: 0.431

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.331

Gnomad OTH AF: 0.297

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

GnomAD4 genome AF: 0.291 AC: 44245 AN: 152000 Hom.: 7083 Cov.: 31 AF XY: 0.297 AC XY: 22031 AN XY: 74302

Gnomad4 AFR AF: 0.160

Gnomad4 AMR AF: 0.313

Gnomad4 ASJ AF: 0.293

Gnomad4 EAS AF: 0.403

Gnomad4 SAS AF: 0.362

Gnomad4 FIN AF: 0.431

Gnomad4 NFE AF: 0.331

Gnomad4 OTH AF: 0.301

Alfa AF: 0.319 Hom.: 16138

Bravo AF: 0.277

Asia WGS AF: 0.381 AC: 1328 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
Cadd	Benign	0.063
Dann	Benign	0.24

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs1157907; hg19: chr2-15004748;