6-43950670-C-T

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SCIRT	ENST00000687158.2	n.520-18494G>A		intron_variant	Intron 3 of 3
SCIRT	ENST00000687455.1	n.234-18494G>A		intron_variant	Intron 2 of 2
SCIRT	ENST00000687843.1	n.593-18494G>A		intron_variant	Intron 4 of 4

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

Gnomad4 AFR AF: 0.129

Gnomad4 AMR AF: 0.455

Gnomad4 ASJ AF: 0.450

Gnomad4 EAS AF: 0.297

Gnomad4 SAS AF: 0.367

Gnomad4 FIN AF: 0.475

Gnomad4 NFE AF: 0.417

Gnomad4 OTH AF: 0.339

Alfa AF: 0.388 Hom.: 10649

Bravo AF: 0.330

Asia WGS AF: 0.324 AC: 1127 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9369434; hg19: chr6-43918407;