rs1053096

Variant names:

• chr2-100996153-T-A
• rs1053096
• NM_002518.4:c.*571T>A

Your query was ambiguous. Multiple possible variants found:

• chr2-100996153-T-A
• chr2-100996153-T-C

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000335681.10(NPAS2):​c.*571T>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: NPAS2 ENST00000335681.10 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.932
• Publications: 13 publications found

Genes affected

NPAS2 (HGNC:7895): (neuronal PAS domain protein 2) The protein encoded by this gene is a member of the basic helix-loop-helix (bHLH)-PAS family of transcription factors. A similar mouse protein may play a regulatory role in the acquisition of specific types of memory. It also may function as a part of a molecular clock operative in the mammalian forebrain. [provided by RefSeq, Jul 2008]

ENSG00000223947 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000335681.10. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NPAS2	NM_002518.4	MANE Select	c.*571T>A		3_prime_UTR	Exon 21 of 21	NP_002509.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NPAS2	ENST00000335681.10	TSL:1 MANE Select	c.*571T>A		3_prime_UTR	Exon 21 of 21	ENSP00000338283.5
	ENSG00000223947	ENST00000452364.1	TSL:1	n.1152-144A>T		intron	N/A
	NPAS2	ENST00000495559.1	TSL:2	n.3165T>A		non_coding_transcript_exon	Exon 4 of 4

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 124178 Hom.: 0 Cov.: 4 AF XY: 0.00 AC XY: 0 AN XY: 64584

African (AFR) AF: 0.00 AC: 0 AN: 3362

American (AMR) AF: 0.00 AC: 0 AN: 4864

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2236

East Asian (EAS) AF: 0.00 AC: 0 AN: 4654

South Asian (SAS) AF: 0.00 AC: 0 AN: 15074

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 3806

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 396

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 84334

Other (OTH) AF: 0.00 AC: 0 AN: 5452

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.055
DANN	Benign	0.25
PhyloP100		-0.93

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: rs1053096; hg19: chr2-101612615;