6-43983599-G-A

Variant names:

• chr6-43983599-G-A
• rs1776717
• ENST00000687158.2:n.519+15619C>T

Variant summary

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

The ENST00000687158.2(SCIRT):​n.519+15619C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.253 in 152,040 control chromosomes in the GnomAD database, including 5,012 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 0.25 (5012 hom., cov: 32)
• Consequence: SCIRT ENST00000687158.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.306
• 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=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.308 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+15619C>T		intron	N/A
	SCIRT	ENST00000687455.2		n.244+17444C>T		intron	N/A
	SCIRT	ENST00000687843.1		n.592+15619C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.253 AC: 38462 AN: 151922 Hom.: 5008 Cov.: 32

Gnomad AFR AF: 0.312

Gnomad AMI AF: 0.336

Gnomad AMR AF: 0.278

Gnomad ASJ AF: 0.213

Gnomad EAS AF: 0.232

Gnomad SAS AF: 0.291

Gnomad FIN AF: 0.222

Gnomad MID AF: 0.213

Gnomad NFE AF: 0.217

Gnomad OTH AF: 0.250

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

GnomAD4 genome AF: 0.253 AC: 38497 AN: 152040 Hom.: 5012 Cov.: 32 AF XY: 0.255 AC XY: 18970 AN XY: 74310

African (AFR) AF: 0.312 AC: 12950 AN: 41464

American (AMR) AF: 0.278 AC: 4252 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.213 AC: 739 AN: 3470

East Asian (EAS) AF: 0.232 AC: 1196 AN: 5152

South Asian (SAS) AF: 0.290 AC: 1396 AN: 4820

European-Finnish (FIN) AF: 0.222 AC: 2348 AN: 10570

Middle Eastern (MID) AF: 0.209 AC: 61 AN: 292

European-Non Finnish (NFE) AF: 0.217 AC: 14721 AN: 67976

Other (OTH) AF: 0.250 AC: 528 AN: 2110

Alfa AF: 0.109 Hom.: 165

Bravo AF: 0.260

Asia WGS AF: 0.290 AC: 1010 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.5
DANN	Benign	0.30
PhyloP100		0.31

Splicing

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

Other links and lift over

dbSNP: rs1776717; hg19: chr6-43951336;