rs2154319

chr1-41280098-T-Cchr1-41280098-T-G

Variant summary

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

The ENST00000445073.1(SCMH1-DT):n.133-4187T>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.148 in 151,892 control chromosomes in the GnomAD database, including 2,158 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 0.15 (2158 hom., cov: 32)
• Consequence: SCMH1-DT ENST00000445073.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.527

Genes affected

SCMH1-DT (HGNC:55675): (SCMH1 divergent transcript)

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.21 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SCMH1-DT	ENST00000445073.1	n.133-4187T>C		intron_variant, non_coding_transcript_variant		3
	ENST00000657314.1	n.205+38122T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.148 AC: 22504 AN: 151774 Hom.: 2157 Cov.: 32

Gnomad AFR AF: 0.0399

Gnomad AMI AF: 0.220

Gnomad AMR AF: 0.144

Gnomad ASJ AF: 0.226

Gnomad EAS AF: 0.0333

Gnomad SAS AF: 0.0829

Gnomad FIN AF: 0.217

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.213

Gnomad OTH AF: 0.152

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

GnomAD4 genome AF: 0.148 AC: 22518 AN: 151892 Hom.: 2158 Cov.: 32 AF XY: 0.149 AC XY: 11081 AN XY: 74226

Gnomad4 AFR AF: 0.0399

Gnomad4 AMR AF: 0.144

Gnomad4 ASJ AF: 0.226

Gnomad4 EAS AF: 0.0336

Gnomad4 SAS AF: 0.0825

Gnomad4 FIN AF: 0.217

Gnomad4 NFE AF: 0.213

Gnomad4 OTH AF: 0.153

Alfa AF: 0.199 Hom.: 3984

Bravo AF: 0.141

Asia WGS AF: 0.0890 AC: 309 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	10
Dann	Benign	0.87

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2154319; hg19: chr1-41745770;