1-25208560-C-T

Variant names:

• chr1-25208560-C-T
• rs77353590
• ENST00000455902.3:n.203C>T

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BP4_Strong BS2

The ENST00000455902.3(ENSG00000231953):​n.203C>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 0.00401 in 116,938 control chromosomes in the GnomAD database, including 6 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 0.0040 (6 hom., cov: 29)
• Consequence: ENSG00000231953 ENST00000455902.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.189
• Publications: 1 publications found

Genes affected

ENSG00000231953 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BS2: High Homozygotes in GnomAd4 at 6 gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000455902.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000231953	ENST00000455902.3	TSL:3	n.203C>T		non_coding_transcript_exon	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.00398 AC: 465 AN: 116896 Hom.: 5 Cov.: 29

Gnomad AFR AF: 0.0151

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00136

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.000183

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000344

Gnomad OTH AF: 0.00326

GnomAD4 exome Cov.: 0

GnomAD4 genome AF: 0.00401 AC: 469 AN: 116938 Hom.: 6 Cov.: 29 AF XY: 0.00396 AC XY: 218 AN XY: 54986

African (AFR) AF: 0.0152 AC: 447 AN: 29440

American (AMR) AF: 0.00136 AC: 14 AN: 10274

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3068

East Asian (EAS) AF: 0.00 AC: 0 AN: 4186

South Asian (SAS) AF: 0.00 AC: 0 AN: 3856

European-Finnish (FIN) AF: 0.000183 AC: 1 AN: 5454

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 162

European-Non Finnish (NFE) AF: 0.0000344 AC: 2 AN: 58170

Other (OTH) AF: 0.00323 AC: 5 AN: 1548

Alfa AF: 0.00305 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.9
DANN	Benign	0.46
PhyloP100		-0.19

Splicing

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

Other links and lift over

dbSNP: rs77353590; hg19: chr1-25535051;