6-107818366-C-T

Position:

• chr6-107818366-C-T

Variant summary

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

The NM_198081.5(SCML4):​c.-60+5760G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0853 in 152,154 control chromosomes in the GnomAD database, including 585 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 0.085 (585 hom., cov: 33)
• Consequence: SCML4 NM_198081.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.751

Genes affected

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]

SCML4 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.121 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SCML4	NM_198081.5	c.-60+5760G>A		intron_variant		ENST00000369020.8	NP_932347.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SCML4	ENST00000369020.8	c.-60+5760G>A		intron_variant		5	NM_198081.5	ENSP00000358016.3

Frequencies

GnomAD3 genomes AF: 0.0853 AC: 12971 AN: 152036 Hom.: 586 Cov.: 33

Gnomad AFR AF: 0.0984

Gnomad AMI AF: 0.118

Gnomad AMR AF: 0.0761

Gnomad ASJ AF: 0.144

Gnomad EAS AF: 0.129

Gnomad SAS AF: 0.0394

Gnomad FIN AF: 0.0898

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.0750

Gnomad OTH AF: 0.0928

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

GnomAD4 genome AF: 0.0853 AC: 12981 AN: 152154 Hom.: 585 Cov.: 33 AF XY: 0.0862 AC XY: 6415 AN XY: 74392

Gnomad4 AFR AF: 0.0983

Gnomad4 AMR AF: 0.0760

Gnomad4 ASJ AF: 0.144

Gnomad4 EAS AF: 0.130

Gnomad4 SAS AF: 0.0396

Gnomad4 FIN AF: 0.0898

Gnomad4 NFE AF: 0.0750

Gnomad4 OTH AF: 0.0942

Alfa AF: 0.0735 Hom.: 675

Bravo AF: 0.0866

Asia WGS AF: 0.0910 AC: 315 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.40
DANN	Benign	0.69

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs17068819; hg19: chr6-108139570;