rs6656085

chr1-41175655-T-Cchr1-41175655-T-G

Variant summary

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

The NM_001394311.1(SCMH1):c.13+10466A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.463 in 152,022 control chromosomes in the GnomAD database, including 18,079 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 0.46 (18079 hom., cov: 31)
• Consequence: SCMH1 NM_001394311.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0720

Genes affected

SCMH1 (HGNC:19003): (Scm polycomb group protein homolog 1) Predicted to enable chromatin binding activity and histone binding activity. Predicted to be involved in negative regulation of transcription, DNA-templated. Predicted to act upstream of or within anterior/posterior pattern specification; chromatin remodeling; and spermatogenesis. Predicted to be located in nucleoplasm. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.588 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SCMH1	NM_001394311.1	c.13+10466A>G		intron_variant		ENST00000695335.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SCMH1	ENST00000695335.1	c.13+10466A>G		intron_variant			NM_001394311.1	A2

Frequencies

GnomAD3 genomes AF: 0.464 AC: 70406 AN: 151900 Hom.: 18068 Cov.: 31

Gnomad AFR AF: 0.226

Gnomad AMI AF: 0.502

Gnomad AMR AF: 0.598

Gnomad ASJ AF: 0.544

Gnomad EAS AF: 0.547

Gnomad SAS AF: 0.517

Gnomad FIN AF: 0.525

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.552

Gnomad OTH AF: 0.506

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

GnomAD4 genome AF: 0.463 AC: 70458 AN: 152022 Hom.: 18079 Cov.: 31 AF XY: 0.467 AC XY: 34688 AN XY: 74318

Gnomad4 AFR AF: 0.226

Gnomad4 AMR AF: 0.598

Gnomad4 ASJ AF: 0.544

Gnomad4 EAS AF: 0.548

Gnomad4 SAS AF: 0.517

Gnomad4 FIN AF: 0.525

Gnomad4 NFE AF: 0.552

Gnomad4 OTH AF: 0.504

Alfa AF: 0.466 Hom.: 2587

Bravo AF: 0.460

Asia WGS AF: 0.501 AC: 1741 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	3.3
Dann	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6656085; hg19: chr1-41641327;