chr6-43951958-C-A

Variant names:

• chr6-43951958-C-A
• rs9472159
• ENST00000687158.2:n.520-19782G>T

Variant summary

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

The ENST00000687158.2(SCIRT):​n.520-19782G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.391 in 152,126 control chromosomes in the GnomAD database, including 13,432 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 0.39 (13432 hom., cov: 33)
• Consequence: SCIRT ENST00000687158.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.194
• Publications: 12 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=-0.78).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.491 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SCIRT	ENST00000687158.2		n.520-19782G>T		intron	N/A
	SCIRT	ENST00000687455.2		n.245-19782G>T		intron	N/A
	SCIRT	ENST00000687843.1		n.593-19782G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.392 AC: 59543 AN: 152008 Hom.: 13433 Cov.: 33

Gnomad AFR AF: 0.155

Gnomad AMI AF: 0.588

Gnomad AMR AF: 0.501

Gnomad ASJ AF: 0.487

Gnomad EAS AF: 0.296

Gnomad SAS AF: 0.410

Gnomad FIN AF: 0.544

Gnomad MID AF: 0.344

Gnomad NFE AF: 0.487

Gnomad OTH AF: 0.391

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

GnomAD4 genome AF: 0.391 AC: 59536 AN: 152126 Hom.: 13432 Cov.: 33 AF XY: 0.397 AC XY: 29511 AN XY: 74366

African (AFR) AF: 0.154 AC: 6407 AN: 41518

American (AMR) AF: 0.501 AC: 7657 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.487 AC: 1688 AN: 3468

East Asian (EAS) AF: 0.295 AC: 1524 AN: 5158

South Asian (SAS) AF: 0.410 AC: 1973 AN: 4818

European-Finnish (FIN) AF: 0.544 AC: 5751 AN: 10580

Middle Eastern (MID) AF: 0.332 AC: 97 AN: 292

European-Non Finnish (NFE) AF: 0.487 AC: 33081 AN: 67974

Other (OTH) AF: 0.389 AC: 822 AN: 2112

Alfa AF: 0.461 Hom.: 34541

Bravo AF: 0.378

Asia WGS AF: 0.329 AC: 1145 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	8.1
DANN	Benign	0.40
PhyloP100		0.19

Splicing

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

Other links and lift over

dbSNP: rs9472159; hg19: chr6-43919695;