rs1776717

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr6-43983599-G-A
• chr6-43983599-G-C

Variant summary

Our verdict is Benign. Variant got -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

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=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.308 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.519+15619C>T		intron_variant	Intron 3 of 3
SCIRT	ENST00000687455.1	n.233+17444C>T		intron_variant	Intron 2 of 2
SCIRT	ENST00000687843.1	n.592+15619C>T		intron_variant	Intron 4 of 4

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

Gnomad4 AFR AF: 0.312

Gnomad4 AMR AF: 0.278

Gnomad4 ASJ AF: 0.213

Gnomad4 EAS AF: 0.232

Gnomad4 SAS AF: 0.290

Gnomad4 FIN AF: 0.222

Gnomad4 NFE AF: 0.217

Gnomad4 OTH AF: 0.250

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1776717; hg19: chr6-43951336;