rs910611

Variant names:

• chr6-43983114-T-C
• rs910611
• ENST00000687158.2:n.519+16104A>G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000687158.2(SCIRT):​n.519+16104A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0804 in 151,998 control chromosomes in the GnomAD database, including 596 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 0.080 (596 hom., cov: 32)
• Consequence: SCIRT ENST00000687158.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.652

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 (SAS) allele frequency at 95% confidence interval = 0.136 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+16104A>G		intron_variant	Intron 3 of 3
SCIRT	ENST00000687455.1	n.233+17929A>G		intron_variant	Intron 2 of 2
SCIRT	ENST00000687843.1	n.592+16104A>G		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.0804 AC: 12207 AN: 151880 Hom.: 590 Cov.: 32

Gnomad AFR AF: 0.0541

Gnomad AMI AF: 0.104

Gnomad AMR AF: 0.105

Gnomad ASJ AF: 0.0854

Gnomad EAS AF: 0.138

Gnomad SAS AF: 0.145

Gnomad FIN AF: 0.0908

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0798

Gnomad OTH AF: 0.0817

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

GnomAD4 genome AF: 0.0804 AC: 12222 AN: 151998 Hom.: 596 Cov.: 32 AF XY: 0.0825 AC XY: 6128 AN XY: 74314

Gnomad4 AFR AF: 0.0541

Gnomad4 AMR AF: 0.105

Gnomad4 ASJ AF: 0.0854

Gnomad4 EAS AF: 0.137

Gnomad4 SAS AF: 0.145

Gnomad4 FIN AF: 0.0908

Gnomad4 NFE AF: 0.0798

Gnomad4 OTH AF: 0.0842

Alfa AF: 0.0826 Hom.: 752

Bravo AF: 0.0809

Asia WGS AF: 0.150 AC: 520 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	0.43
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs910611; hg19: chr6-43950851;