1-41096613-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.745+16670A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.849 in 152,096 control chromosomes in the GnomAD database, including 55,340 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 0.85 (55340 hom., cov: 30)
• Consequence: SCMH1 NM_001394311.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.722

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=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.948 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SCMH1	NM_001394311.1	c.745+16670A>C		intron_variant		ENST00000695335.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SCMH1	ENST00000695335.1	c.745+16670A>C		intron_variant			NM_001394311.1	A2

Frequencies

GnomAD3 genomes AF: 0.849 AC: 129072 AN: 151976 Hom.: 55292 Cov.: 30

Gnomad AFR AF: 0.956

Gnomad AMI AF: 0.726

Gnomad AMR AF: 0.852

Gnomad ASJ AF: 0.781

Gnomad EAS AF: 0.965

Gnomad SAS AF: 0.905

Gnomad FIN AF: 0.784

Gnomad MID AF: 0.857

Gnomad NFE AF: 0.786

Gnomad OTH AF: 0.851

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

GnomAD4 genome AF: 0.849 AC: 129179 AN: 152096 Hom.: 55340 Cov.: 30 AF XY: 0.848 AC XY: 63055 AN XY: 74340

Gnomad4 AFR AF: 0.956

Gnomad4 AMR AF: 0.852

Gnomad4 ASJ AF: 0.781

Gnomad4 EAS AF: 0.965

Gnomad4 SAS AF: 0.905

Gnomad4 FIN AF: 0.784

Gnomad4 NFE AF: 0.786

Gnomad4 OTH AF: 0.849

Alfa AF: 0.750 Hom.: 2308

Bravo AF: 0.856

Asia WGS AF: 0.910 AC: 3165 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	0.96
Dann	Benign	0.60

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs2024859; hg19: chr1-41562285;