6-43950670-C-T

Variant names:

• chr6-43950670-C-T
• rs9369434
• ENST00000687158.2:n.520-18494G>A

Variant summary

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

The ENST00000687158.2(SCIRT):​n.520-18494G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.34 in 151,990 control chromosomes in the GnomAD database, including 10,307 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 0.34 (10307 hom., cov: 32)
• Consequence: SCIRT ENST00000687158.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.66
• Publications: 6 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=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.446 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.520-18494G>A		intron	N/A
	SCIRT	ENST00000687455.2		n.245-18494G>A		intron	N/A
	SCIRT	ENST00000687843.1		n.593-18494G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.341 AC: 51755 AN: 151872 Hom.: 10308 Cov.: 32

Gnomad AFR AF: 0.129

Gnomad AMI AF: 0.530

Gnomad AMR AF: 0.455

Gnomad ASJ AF: 0.450

Gnomad EAS AF: 0.298

Gnomad SAS AF: 0.368

Gnomad FIN AF: 0.475

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.417

Gnomad OTH AF: 0.341

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

GnomAD4 genome AF: 0.340 AC: 51750 AN: 151990 Hom.: 10307 Cov.: 32 AF XY: 0.345 AC XY: 25655 AN XY: 74296

African (AFR) AF: 0.129 AC: 5364 AN: 41490

American (AMR) AF: 0.455 AC: 6947 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.450 AC: 1560 AN: 3470

East Asian (EAS) AF: 0.297 AC: 1532 AN: 5154

South Asian (SAS) AF: 0.367 AC: 1768 AN: 4814

European-Finnish (FIN) AF: 0.475 AC: 5011 AN: 10560

Middle Eastern (MID) AF: 0.272 AC: 80 AN: 294

European-Non Finnish (NFE) AF: 0.417 AC: 28292 AN: 67922

Other (OTH) AF: 0.339 AC: 714 AN: 2106

Alfa AF: 0.381 Hom.: 13679

Bravo AF: 0.330

Asia WGS AF: 0.324 AC: 1127 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.30
DANN	Benign	0.69
PhyloP100		-1.7

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: rs9369434;

hg19: chr6-43918407;