1-41272965-C-T

Variant names:

• chr1-41272965-C-T
• rs4131949
• ENST00000670398.1:n.555C>T

Variant summary

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

The ENST00000670398.1(SCMH1-DT):​n.555C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.109 in 152,182 control chromosomes in the GnomAD database, including 1,273 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 0.11 (1273 hom., cov: 33)
• Consequence: SCMH1-DT ENST00000670398.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0820
• Publications: 4 publications found

Genes affected

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.259 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SCMH1-DT	ENST00000670398.1	n.555C>T		non_coding_transcript_exon_variant	Exon 3 of 3
SCMH1-DT	ENST00000847546.1	n.622C>T		non_coding_transcript_exon_variant	Exon 2 of 2
SCMH1-DT	ENST00000445073.1	n.133-11320C>T		intron_variant	Intron 1 of 1	3

Frequencies

GnomAD3 genomes AF: 0.109 AC: 16592 AN: 152064 Hom.: 1269 Cov.: 33

Gnomad AFR AF: 0.0315

Gnomad AMI AF: 0.0396

Gnomad AMR AF: 0.236

Gnomad ASJ AF: 0.108

Gnomad EAS AF: 0.270

Gnomad SAS AF: 0.113

Gnomad FIN AF: 0.116

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.115

Gnomad OTH AF: 0.123

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

GnomAD4 genome AF: 0.109 AC: 16600 AN: 152182 Hom.: 1273 Cov.: 33 AF XY: 0.113 AC XY: 8425 AN XY: 74386

African (AFR) AF: 0.0314 AC: 1305 AN: 41538

American (AMR) AF: 0.236 AC: 3608 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.108 AC: 375 AN: 3468

East Asian (EAS) AF: 0.271 AC: 1400 AN: 5172

South Asian (SAS) AF: 0.114 AC: 548 AN: 4822

European-Finnish (FIN) AF: 0.116 AC: 1230 AN: 10584

Middle Eastern (MID) AF: 0.109 AC: 32 AN: 294

European-Non Finnish (NFE) AF: 0.115 AC: 7808 AN: 67990

Other (OTH) AF: 0.122 AC: 258 AN: 2114

Alfa AF: 0.0769 Hom.: 149

Bravo AF: 0.115

Asia WGS AF: 0.160 AC: 555 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	5.7
DANN	Benign	0.77
PhyloP100		0.082

Splicing

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

Other links and lift over

dbSNP: rs4131949; hg19: chr1-41738637;