1-41098016-C-T

Variant names:

• chr1-41098016-C-T
• rs6663565
• NM_001394311.1:c.745+15267G>A

Variant summary

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

The NM_001394311.1(SCMH1):​c.745+15267G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.643 in 152,028 control chromosomes in the GnomAD database, including 32,815 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 0.64 (32815 hom., cov: 32)
• Consequence: SCMH1 NM_001394311.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.34
• Publications: 9 publications found

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

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.833 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001394311.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SCMH1	NM_001394311.1	MANE Select	c.745+15267G>A		intron	N/A	NP_001381240.1	A0A8Q3SHN2
	SCMH1	NM_001031694.3		c.715+15267G>A		intron	N/A	NP_001026864.1	Q96GD3-1
	SCMH1	NM_001394300.1		c.715+15267G>A		intron	N/A	NP_001381229.1	Q96GD3-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SCMH1	ENST00000695335.1	MANE Select	c.745+15267G>A		intron	N/A	ENSP00000511813.1	A0A8Q3SHN2
	SCMH1	ENST00000326197.11	TSL:1	c.715+15267G>A		intron	N/A	ENSP00000318094.7	Q96GD3-1
	SCMH1	ENST00000372595.5	TSL:1	c.532+15267G>A		intron	N/A	ENSP00000361676.1	Q96GD3-3

Frequencies

GnomAD3 genomes AF: 0.643 AC: 97688 AN: 151912 Hom.: 32761 Cov.: 32

Gnomad AFR AF: 0.840

Gnomad AMI AF: 0.663

Gnomad AMR AF: 0.496

Gnomad ASJ AF: 0.597

Gnomad EAS AF: 0.583

Gnomad SAS AF: 0.665

Gnomad FIN AF: 0.562

Gnomad MID AF: 0.684

Gnomad NFE AF: 0.574

Gnomad OTH AF: 0.624

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

GnomAD4 genome AF: 0.643 AC: 97798 AN: 152028 Hom.: 32815 Cov.: 32 AF XY: 0.638 AC XY: 47408 AN XY: 74304

African (AFR) AF: 0.841 AC: 34876 AN: 41488

American (AMR) AF: 0.495 AC: 7560 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.597 AC: 2072 AN: 3468

East Asian (EAS) AF: 0.584 AC: 3016 AN: 5168

South Asian (SAS) AF: 0.665 AC: 3205 AN: 4818

European-Finnish (FIN) AF: 0.562 AC: 5926 AN: 10546

Middle Eastern (MID) AF: 0.687 AC: 202 AN: 294

European-Non Finnish (NFE) AF: 0.574 AC: 39016 AN: 67960

Other (OTH) AF: 0.625 AC: 1322 AN: 2114

Alfa AF: 0.605 Hom.: 15190

Bravo AF: 0.642

Asia WGS AF: 0.662 AC: 2305 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.63
DANN	Benign	0.60
PhyloP100		-1.3
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs6663565; hg19: chr1-41563688; COSMIC: COSV58233647; COSMIC: COSV58233647;