chr1-41272965-C-T

Position:

• chr1-41272965-C-T

Variant summary

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

The ENST00000445073.1(SCMH1-DT):​n.133-11320C>T 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 0.109 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 ENST00000445073.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0820

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=-0.76).
• 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SCMH1-DT	ENST00000445073.1	n.133-11320C>T		intron_variant, non_coding_transcript_variant		3
	ENST00000657314.1	n.205+30989C>T		intron_variant, non_coding_transcript_variant
SCMH1-DT	ENST00000670398.1	n.555C>T		non_coding_transcript_exon_variant	3/3

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

Gnomad4 AFR AF: 0.0314

Gnomad4 AMR AF: 0.236

Gnomad4 ASJ AF: 0.108

Gnomad4 EAS AF: 0.271

Gnomad4 SAS AF: 0.114

Gnomad4 FIN AF: 0.116

Gnomad4 NFE AF: 0.115

Gnomad4 OTH AF: 0.122

Alfa AF: 0.106 Hom.: 124

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4131949; hg19: chr1-41738637;