rs1519511

Variant names:

• chr2-87648433-G-A
• rs1519511
• ENST00000776920.1:n.823C>T

Your query was ambiguous. Multiple possible variants found:

• chr2-87648433-G-A
• chr2-87648433-G-C
• chr2-87648433-G-T

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BP4_Strong BS2

The ENST00000776920.1(ENSG00000289429):​n.823C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.463 in 133,656 control chromosomes in the GnomAD database, including 15,471 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 0.46 (15471 hom., cov: 23)
• Consequence: ENSG00000289429 ENST00000776920.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.23
• Publications: 0 publications found

Genes affected

ENSG00000289429 (HGNC:):

NCAL1 (HGNC:56663): (NK cell activity associated lncRNA 1)

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BS2: High Homozygotes in GnomAd4 at 15471 gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000776920.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NCAL1	NR_186253.1		n.344+41664G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000289429	ENST00000776920.1		n.823C>T		non_coding_transcript_exon	Exon 4 of 4
	ENSG00000289429	ENST00000776921.1		n.646C>T		non_coding_transcript_exon	Exon 4 of 4
	ENSG00000289429	ENST00000776922.1		n.1103C>T		non_coding_transcript_exon	Exon 5 of 5

Frequencies

GnomAD3 genomes AF: 0.463 AC: 61861 AN: 133526 Hom.: 15455 Cov.: 23

Gnomad AFR AF: 0.599

Gnomad AMI AF: 0.551

Gnomad AMR AF: 0.417

Gnomad ASJ AF: 0.376

Gnomad EAS AF: 0.587

Gnomad SAS AF: 0.390

Gnomad FIN AF: 0.371

Gnomad MID AF: 0.312

Gnomad NFE AF: 0.411

Gnomad OTH AF: 0.431

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

GnomAD4 genome AF: 0.463 AC: 61930 AN: 133656 Hom.: 15471 Cov.: 23 AF XY: 0.460 AC XY: 29857 AN XY: 64950

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.599 AC: 21213 AN: 35434

American (AMR) AF: 0.416 AC: 5627 AN: 13536

Ashkenazi Jewish (ASJ) AF: 0.376 AC: 1167 AN: 3104

East Asian (EAS) AF: 0.586 AC: 2426 AN: 4138

South Asian (SAS) AF: 0.390 AC: 1590 AN: 4074

European-Finnish (FIN) AF: 0.371 AC: 3393 AN: 9152

Middle Eastern (MID) AF: 0.297 AC: 73 AN: 246

European-Non Finnish (NFE) AF: 0.411 AC: 25206 AN: 61348

Other (OTH) AF: 0.434 AC: 781 AN: 1800

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

Alfa AF: 0.263 Hom.: 510

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.014
DANN	Benign	0.61
PhyloP100		-3.2

Splicing

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

Other links and lift over

dbSNP: rs1519511; hg19: chr2-87947952;