chr6-43983114-T-C

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 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=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.136 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.519+16104A>G		intron	N/A
	SCIRT	ENST00000687455.2		n.244+17929A>G		intron	N/A
	SCIRT	ENST00000687843.1		n.592+16104A>G		intron	N/A

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

African (AFR) AF: 0.0541 AC: 2243 AN: 41446

American (AMR) AF: 0.105 AC: 1604 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.0854 AC: 296 AN: 3466

East Asian (EAS) AF: 0.137 AC: 709 AN: 5162

South Asian (SAS) AF: 0.145 AC: 696 AN: 4808

European-Finnish (FIN) AF: 0.0908 AC: 960 AN: 10568

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.0798 AC: 5426 AN: 67968

Other (OTH) AF: 0.0842 AC: 178 AN: 2114

Alfa AF: 0.0811 Hom.: 1069

Bravo AF: 0.0809

Asia WGS AF: 0.150 AC: 520 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.43
DANN	Benign	0.61
PhyloP100		-0.65

Splicing

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

Other links and lift over

dbSNP: rs910611; hg19: chr6-43950851;