rs2066432

Variant names:

• chr6-43966925-C-T
• rs2066432
• ENST00000687158.2:n.519+32293G>A

Variant summary

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

The ENST00000687158.2(SCIRT):​n.519+32293G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.507 in 151,934 control chromosomes in the GnomAD database, including 19,984 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 0.51 (19984 hom., cov: 33)
• Consequence: SCIRT ENST00000687158.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.147
• Publications: 2 publications found

Genes affected

SCIRT (HGNC:55341): (stem cell inhibitory RNA transcript)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.788 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000687158.2. 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
	SCIRT	ENST00000687158.2		n.519+32293G>A		intron	N/A
	SCIRT	ENST00000687455.2		n.244+34118G>A		intron	N/A
	SCIRT	ENST00000687843.1		n.592+32293G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.508 AC: 77051 AN: 151816 Hom.: 19972 Cov.: 33

Gnomad AFR AF: 0.458

Gnomad AMI AF: 0.560

Gnomad AMR AF: 0.599

Gnomad ASJ AF: 0.505

Gnomad EAS AF: 0.809

Gnomad SAS AF: 0.631

Gnomad FIN AF: 0.441

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.495

Gnomad OTH AF: 0.522

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

GnomAD4 genome AF: 0.507 AC: 77094 AN: 151934 Hom.: 19984 Cov.: 33 AF XY: 0.514 AC XY: 38184 AN XY: 74278

African (AFR) AF: 0.457 AC: 18914 AN: 41368

American (AMR) AF: 0.599 AC: 9158 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.505 AC: 1752 AN: 3470

East Asian (EAS) AF: 0.809 AC: 4180 AN: 5170

South Asian (SAS) AF: 0.632 AC: 3044 AN: 4820

European-Finnish (FIN) AF: 0.441 AC: 4657 AN: 10566

Middle Eastern (MID) AF: 0.517 AC: 152 AN: 294

European-Non Finnish (NFE) AF: 0.495 AC: 33621 AN: 67942

Other (OTH) AF: 0.525 AC: 1106 AN: 2108

Alfa AF: 0.506 Hom.: 34139

Bravo AF: 0.516

Asia WGS AF: 0.678 AC: 2357 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.6
DANN	Benign	0.42
PhyloP100		0.15

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: rs2066432;

hg19: chr6-43934662;