rs3734693

chr6-43997428-T-C

Variant summary

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

The NR_125864.1(SCIRT):n.647-120A>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.346 in 152,092 control chromosomes in the GnomAD database, including 13,667 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 0.35 (13666 hom., cov: 32)
  • Exomes 𝑓: 0.15 (1 hom.)
• Consequence: SCIRT NR_125864.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.69

Genes affected

SCIRT (HGNC:55341): (stem cell inhibitory RNA transcript)

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.57).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.719 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SCIRT	NR_125864.1	n.647-120A>G		intron_variant, non_coding_transcript_variant
LOC124901321	XR_007059591.1	n.43-1523T>C		intron_variant, non_coding_transcript_variant
POLR1C	NM_001318876.2	c.946-444462T>C		intron_variant
SCIRT	NR_125865.1	n.431-120A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SCIRT	ENST00000687455.1	n.233+3615A>G		intron_variant, non_coding_transcript_variant
	ENST00000690796.2	n.72-1523T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.346 AC: 52534 AN: 151902 Hom.: 13612 Cov.: 32

Gnomad AFR AF: 0.726

Gnomad AMI AF: 0.144

Gnomad AMR AF: 0.281

Gnomad ASJ AF: 0.312

Gnomad EAS AF: 0.394

Gnomad SAS AF: 0.348

Gnomad FIN AF: 0.153

Gnomad MID AF: 0.361

Gnomad NFE AF: 0.161

Gnomad OTH AF: 0.320

GnomAD4 exome AF: 0.153 AC: 11 AN: 72 Hom.: 1 AF XY: 0.196 AC XY: 11 AN XY: 56

Gnomad4 AMR exome AF: 0.00

Gnomad4 SAS exome AF: 0.500

Gnomad4 FIN exome AF: 0.182

Gnomad4 NFE exome AF: 0.158

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.346 AC: 52657 AN: 152020 Hom.: 13666 Cov.: 32 AF XY: 0.346 AC XY: 25698 AN XY: 74300

Gnomad4 AFR AF: 0.726

Gnomad4 AMR AF: 0.282

Gnomad4 ASJ AF: 0.312

Gnomad4 EAS AF: 0.394

Gnomad4 SAS AF: 0.348

Gnomad4 FIN AF: 0.153

Gnomad4 NFE AF: 0.161

Gnomad4 OTH AF: 0.324

Alfa AF: 0.194 Hom.: 7554

Bravo AF: 0.373

Asia WGS AF: 0.416 AC: 1449 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.57
Cadd	Benign	16
Dann	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3734693; hg19: chr6-43965165;