ENST00000805070.1:n.404+15497C>T

Variant names:

• chr6-107830325-G-A
• rs9320240
• ENST00000805070.1:n.404+15497C>T

Variant summary

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

The ENST00000805070.1(ENSG00000304634):​n.404+15497C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.147 in 152,144 control chromosomes in the GnomAD database, including 2,935 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 0.15 (2935 hom., cov: 32)
• Consequence: ENSG00000304634 ENST00000805070.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.559
• Publications: 3 publications found

Genes affected

ENSG00000304634 (HGNC:):

SCML4 (HGNC:21397): (Scm polycomb group protein like 4) Predicted to enable chromatin binding activity and histone binding activity. Predicted to be involved in negative regulation of transcription, DNA-templated. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.347 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SCML4	XM_047418598.1	c.-60+15497C>T		intron_variant	Intron 1 of 9		XP_047274554.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000304634	ENST00000805070.1	n.404+15497C>T		intron_variant	Intron 2 of 2
ENSG00000304634	ENST00000805071.1	n.129-14646C>T		intron_variant	Intron 1 of 1
ENSG00000304634	ENST00000805072.1	n.350-1114C>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.147 AC: 22276 AN: 152026 Hom.: 2930 Cov.: 32

Gnomad AFR AF: 0.352

Gnomad AMI AF: 0.118

Gnomad AMR AF: 0.0839

Gnomad ASJ AF: 0.125

Gnomad EAS AF: 0.0194

Gnomad SAS AF: 0.0333

Gnomad FIN AF: 0.0799

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.0666

Gnomad OTH AF: 0.124

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

GnomAD4 genome AF: 0.147 AC: 22321 AN: 152144 Hom.: 2935 Cov.: 32 AF XY: 0.145 AC XY: 10772 AN XY: 74400

African (AFR) AF: 0.352 AC: 14576 AN: 41442

American (AMR) AF: 0.0838 AC: 1281 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.125 AC: 434 AN: 3472

East Asian (EAS) AF: 0.0195 AC: 101 AN: 5184

South Asian (SAS) AF: 0.0333 AC: 161 AN: 4830

European-Finnish (FIN) AF: 0.0799 AC: 847 AN: 10602

Middle Eastern (MID) AF: 0.0748 AC: 22 AN: 294

European-Non Finnish (NFE) AF: 0.0666 AC: 4527 AN: 68010

Other (OTH) AF: 0.125 AC: 264 AN: 2112

Alfa AF: 0.0957 Hom.: 1041

Bravo AF: 0.157

Asia WGS AF: 0.0460 AC: 159 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	17
DANN	Benign	0.74
PhyloP100		0.56

Splicing

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

Other links and lift over

dbSNP: rs9320240; hg19: chr6-108151529;