rs710411

Variant names:

• chr9-136549504-G-A
• rs710411
• ENST00000429224.2:n.815G>A

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000743457.1(NALT1):​n.904G>A 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 0.598 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 ENST00000743457.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.104
• Publications: 5 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000743457.1. 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
	NALT1	NR_121577.1		n.348-42G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NALT1	ENST00000429224.2	TSL:5	n.815G>A		non_coding_transcript_exon	Exon 3 of 3
	NALT1	ENST00000743457.1		n.904G>A		non_coding_transcript_exon	Exon 4 of 4
	NALT1	ENST00000743459.1		n.813G>A		non_coding_transcript_exon	Exon 6 of 6

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

African (AFR) AF: 0.500 AC: 1 AN: 2

American (AMR) AF: 0.00 AC: 0 AN: 2

Ashkenazi Jewish (ASJ) AF: 1.00 AC: 2 AN: 2

East Asian (EAS) AF: 0.500 AC: 1 AN: 2

South Asian (SAS) AF: 0.611 AC: 22 AN: 36

European-Finnish (FIN) AF: 0.500 AC: 1 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.686 AC: 81 AN: 118

Other (OTH) AF: 0.833 AC: 5 AN: 6

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

African (AFR) AF: 0.508 AC: 21043 AN: 41440

American (AMR) AF: 0.549 AC: 8386 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.728 AC: 2526 AN: 3472

East Asian (EAS) AF: 0.638 AC: 3292 AN: 5158

South Asian (SAS) AF: 0.573 AC: 2764 AN: 4824

European-Finnish (FIN) AF: 0.651 AC: 6887 AN: 10572

Middle Eastern (MID) AF: 0.636 AC: 187 AN: 294

European-Non Finnish (NFE) AF: 0.647 AC: 43979 AN: 67948

Other (OTH) AF: 0.614 AC: 1294 AN: 2108

Alfa AF: 0.626 Hom.: 102569

Bravo AF: 0.584

Asia WGS AF: 0.578 AC: 2011 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.2
DANN	Benign	0.18
PhyloP100		-0.10

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs710411;

hg19: chr9-139443956;