rs1524668

Variant names:

• chr2-9557243-A-C
• rs1524668
• ENST00000607241.2:n.1370A>C

Variant summary

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

The ENST00000607241.2(ENSG00000271855):​n.1370A>C 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 0.63 in 151,838 control chromosomes in the GnomAD database, including 31,513 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (no stars).

• Frequency: Genomes: 𝑓 0.63 (31513 hom., cov: 30)
• Consequence: ENSG00000271855 ENST00000607241.2 non_coding_transcript_exon
• Clinical Significance: Uncertain significance no assertion criteria provided U:1
• Conservation: PhyloP100: -2.08
• Publications: 18 publications found

Genes affected

ENSG00000271855 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.707 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000607241.2. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000271855	ENST00000607241.2	TSL:6	n.1370A>C		non_coding_transcript_exon	Exon 1 of 1
	ENSG00000271855	ENST00000716659.1		n.307+651A>C		intron	N/A
	ENSG00000271855	ENST00000716660.1		n.278+651A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.630 AC: 95527 AN: 151720 Hom.: 31482 Cov.: 30

Gnomad AFR AF: 0.714

Gnomad AMI AF: 0.851

Gnomad AMR AF: 0.490

Gnomad ASJ AF: 0.690

Gnomad EAS AF: 0.0927

Gnomad SAS AF: 0.449

Gnomad FIN AF: 0.529

Gnomad MID AF: 0.758

Gnomad NFE AF: 0.672

Gnomad OTH AF: 0.653

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

GnomAD4 genome AF: 0.630 AC: 95603 AN: 151838 Hom.: 31513 Cov.: 30 AF XY: 0.615 AC XY: 45581 AN XY: 74132

African (AFR) AF: 0.714 AC: 29546 AN: 41384

American (AMR) AF: 0.489 AC: 7457 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.690 AC: 2395 AN: 3472

East Asian (EAS) AF: 0.0923 AC: 477 AN: 5168

South Asian (SAS) AF: 0.448 AC: 2150 AN: 4800

European-Finnish (FIN) AF: 0.529 AC: 5556 AN: 10502

Middle Eastern (MID) AF: 0.760 AC: 222 AN: 292

European-Non Finnish (NFE) AF: 0.672 AC: 45659 AN: 67952

Other (OTH) AF: 0.649 AC: 1365 AN: 2104

Alfa AF: 0.649 Hom.: 13743

Bravo AF: 0.628

Asia WGS AF: 0.315 AC: 1097 AN: 3478

ClinVar

ClinVar submissions

Significance: Uncertain significance

Revision: no assertion criteria provided

Pathogenic	VUS	Benign	Condition
-	1	-	Mycobacterium tuberculosis, susceptibility to (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.46
DANN	Benign	0.65
PhyloP100		-2.1

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: rs1524668;

hg19: chr2-9697372;