rs710411

Positions:

• chr9-136549504-G-A
• chr9-136549504-G-C
• chr9-136549504-G-T

Variant summary

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

The NR_121577.1(NALT1):​n.348-42G>A 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 0.598 in 152,180 control chromosomes in the GnomAD database, including 27,573 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 0.60 (27535 hom., cov: 32)
  • Exomes 𝑓: 0.66 (38 hom.)
• Consequence: NALT1 NR_121577.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.104

Genes affected

NALT1 (HGNC:51192): (NOTCH1 associated lncRNA in T cell acute lymphoblastic leukemia 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.642 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NALT1	NR_121577.1	n.348-42G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NALT1	ENST00000450304.1	n.90-42G>A		intron_variant, non_coding_transcript_variant		3
NALT1	ENST00000701978.1	n.588-42G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.598 AC: 90863 AN: 151892 Hom.: 27534 Cov.: 32

Gnomad AFR AF: 0.508

Gnomad AMI AF: 0.595

Gnomad AMR AF: 0.548

Gnomad ASJ AF: 0.728

Gnomad EAS AF: 0.637

Gnomad SAS AF: 0.575

Gnomad FIN AF: 0.651

Gnomad MID AF: 0.623

Gnomad NFE AF: 0.647

Gnomad OTH AF: 0.615

GnomAD4 exome AF: 0.665 AC: 113 AN: 170 Hom.: 38 Cov.: 0 AF XY: 0.694 AC XY: 93 AN XY: 134

Gnomad4 AFR exome AF: 0.500

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 1.00

Gnomad4 EAS exome AF: 0.500

Gnomad4 SAS exome AF: 0.611

Gnomad4 FIN exome AF: 0.500

Gnomad4 NFE exome AF: 0.686

Gnomad4 OTH exome AF: 0.833

GnomAD4 genome AF: 0.598 AC: 90898 AN: 152010 Hom.: 27535 Cov.: 32 AF XY: 0.597 AC XY: 44395 AN XY: 74318

Gnomad4 AFR AF: 0.508

Gnomad4 AMR AF: 0.549

Gnomad4 ASJ AF: 0.728

Gnomad4 EAS AF: 0.638

Gnomad4 SAS AF: 0.573

Gnomad4 FIN AF: 0.651

Gnomad4 NFE AF: 0.647

Gnomad4 OTH AF: 0.614

Alfa AF: 0.626 Hom.: 36176

Bravo AF: 0.584

Asia WGS AF: 0.578 AC: 2011 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.2
DANN	Benign	0.18

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs710411; hg19: chr9-139443956;