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

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
ENSG00000231953	ENST00000455902.3	n.203C>T		non_coding_transcript_exon_variant	Exon 2 of 2	3

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 v4.3

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;