chr6-43957870-G-A

Variant names:

• chr6-43957870-G-A
• rs6921438
• ENST00000687158.2:n.520-25694C>T

Variant summary

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

The ENST00000687158.2(SCIRT):​n.520-25694C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.466 in 151,762 control chromosomes in the GnomAD database, including 16,580 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 0.47 (16580 hom., cov: 31)
• Consequence: SCIRT ENST00000687158.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.510
• Publications: 57 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.545 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.520-25694C>T		intron	N/A
	SCIRT	ENST00000687455.2		n.245-25694C>T		intron	N/A
	SCIRT	ENST00000687843.1		n.593-25694C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.466 AC: 70644 AN: 151644 Hom.: 16564 Cov.: 31

Gnomad AFR AF: 0.428

Gnomad AMI AF: 0.600

Gnomad AMR AF: 0.554

Gnomad ASJ AF: 0.444

Gnomad EAS AF: 0.376

Gnomad SAS AF: 0.408

Gnomad FIN AF: 0.490

Gnomad MID AF: 0.360

Gnomad NFE AF: 0.477

Gnomad OTH AF: 0.454

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

GnomAD4 genome AF: 0.466 AC: 70683 AN: 151762 Hom.: 16580 Cov.: 31 AF XY: 0.466 AC XY: 34562 AN XY: 74160

African (AFR) AF: 0.427 AC: 17664 AN: 41346

American (AMR) AF: 0.554 AC: 8458 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.444 AC: 1539 AN: 3468

East Asian (EAS) AF: 0.375 AC: 1936 AN: 5158

South Asian (SAS) AF: 0.408 AC: 1959 AN: 4798

European-Finnish (FIN) AF: 0.490 AC: 5157 AN: 10534

Middle Eastern (MID) AF: 0.342 AC: 100 AN: 292

European-Non Finnish (NFE) AF: 0.477 AC: 32362 AN: 67894

Other (OTH) AF: 0.456 AC: 963 AN: 2110

Alfa AF: 0.400 Hom.: 1740

Bravo AF: 0.470

Asia WGS AF: 0.413 AC: 1436 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.5
DANN	Benign	0.76
PhyloP100		0.51

Splicing

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

Other links and lift over

dbSNP: rs6921438; hg19: chr6-43925607;