rs3734693

Variant names:

• chr6-43997428-T-C
• rs3734693
• ENST00000422059.5:n.647-120A>G

Variant summary

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

The ENST00000422059.5(SCIRT):​n.647-120A>G variant causes a intron 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 ENST00000422059.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.69
• Publications: 6 publications found

Genes affected

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

ENSG00000289609 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000422059.5. 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
	SCIRT	NR_125864.1		n.647-120A>G		intron	N/A
	SCIRT	NR_125865.1		n.431-120A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SCIRT	ENST00000422059.5	TSL:2	n.647-120A>G		intron	N/A
	SCIRT	ENST00000607590.1	TSL:3	n.430-120A>G		intron	N/A
	SCIRT	ENST00000652850.2		n.520-120A>G		intron	N/A

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

African (AFR) AC: 0 AN: 0

American (AMR) AF: 0.00 AC: 0 AN: 2

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AF: 0.500 AC: 1 AN: 2

European-Finnish (FIN) AF: 0.182 AC: 4 AN: 22

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.158 AC: 6 AN: 38

Other (OTH) AF: 0.00 AC: 0 AN: 8

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

African (AFR) AF: 0.726 AC: 30089 AN: 41436

American (AMR) AF: 0.282 AC: 4307 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.312 AC: 1083 AN: 3472

East Asian (EAS) AF: 0.394 AC: 2035 AN: 5160

South Asian (SAS) AF: 0.348 AC: 1675 AN: 4816

European-Finnish (FIN) AF: 0.153 AC: 1618 AN: 10572

Middle Eastern (MID) AF: 0.361 AC: 106 AN: 294

European-Non Finnish (NFE) AF: 0.161 AC: 10929 AN: 67964

Other (OTH) AF: 0.324 AC: 684 AN: 2110

Alfa AF: 0.229 Hom.: 18728

Bravo AF: 0.373

Asia WGS AF: 0.416 AC: 1449 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.57
CADD	Benign	16
DANN	Benign	0.73
PhyloP100		1.7

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs3734693;

hg19: chr6-43965165;