1-41223266-C-T

Position:

• chr1-41223266-C-T

Variant summary

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

The NM_001394311.1(SCMH1):​c.-118+18793G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.356 in 152,054 control chromosomes in the GnomAD database, including 11,014 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 0.36 (11014 hom., cov: 32)
• Consequence: SCMH1 NM_001394311.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.04

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=-1.03).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.496 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SCMH1	NM_001394311.1	c.-118+18793G>A		intron_variant		ENST00000695335.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SCMH1	ENST00000695335.1	c.-118+18793G>A		intron_variant			NM_001394311.1	A2

Frequencies

GnomAD3 genomes AF: 0.356 AC: 54150 AN: 151934 Hom.: 11011 Cov.: 32

Gnomad AFR AF: 0.158

Gnomad AMI AF: 0.339

Gnomad AMR AF: 0.505

Gnomad ASJ AF: 0.403

Gnomad EAS AF: 0.413

Gnomad SAS AF: 0.335

Gnomad FIN AF: 0.439

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.426

Gnomad OTH AF: 0.378

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

GnomAD4 genome AF: 0.356 AC: 54158 AN: 152054 Hom.: 11014 Cov.: 32 AF XY: 0.362 AC XY: 26876 AN XY: 74320

Gnomad4 AFR AF: 0.157

Gnomad4 AMR AF: 0.505

Gnomad4 ASJ AF: 0.403

Gnomad4 EAS AF: 0.414

Gnomad4 SAS AF: 0.334

Gnomad4 FIN AF: 0.439

Gnomad4 NFE AF: 0.426

Gnomad4 OTH AF: 0.376

Alfa AF: 0.227 Hom.: 665

Bravo AF: 0.357

Asia WGS AF: 0.338 AC: 1174 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.58
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11209718; hg19: chr1-41688938;