1-94542362-C-T

Variant names:

• chr1-94542362-C-T
• rs1361600
• ENST00000689973.3:n.480C>T

Variant summary

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

The ENST00000837459.1(ENSG00000308945):​n.231G>A variant causes a splice region, non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.514 in 152,008 control chromosomes in the GnomAD database, including 20,888 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 0.51 (20888 hom., cov: 32)
• Consequence: ENSG00000308945 ENST00000837459.1 splice_region, non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.682
• Publications: 17 publications found

Genes affected

ENSG00000288736 (HGNC:):

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 = 0.794 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000837459.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000288736	ENST00000689973.3		n.480C>T		non_coding_transcript_exon	Exon 1 of 1
	ENSG00000288736	ENST00000690142.2		n.142C>T		non_coding_transcript_exon	Exon 2 of 2
	ENSG00000288736	ENST00000690992.2		n.389C>T		non_coding_transcript_exon	Exon 1 of 2

Frequencies

GnomAD3 genomes AF: 0.514 AC: 78088 AN: 151890 Hom.: 20883 Cov.: 32

Gnomad AFR AF: 0.392

Gnomad AMI AF: 0.372

Gnomad AMR AF: 0.541

Gnomad ASJ AF: 0.595

Gnomad EAS AF: 0.815

Gnomad SAS AF: 0.617

Gnomad FIN AF: 0.619

Gnomad MID AF: 0.456

Gnomad NFE AF: 0.535

Gnomad OTH AF: 0.477

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

GnomAD4 genome AF: 0.514 AC: 78131 AN: 152008 Hom.: 20888 Cov.: 32 AF XY: 0.523 AC XY: 38857 AN XY: 74308

African (AFR) AF: 0.391 AC: 16220 AN: 41442

American (AMR) AF: 0.541 AC: 8276 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.595 AC: 2062 AN: 3468

East Asian (EAS) AF: 0.815 AC: 4182 AN: 5132

South Asian (SAS) AF: 0.616 AC: 2972 AN: 4822

European-Finnish (FIN) AF: 0.619 AC: 6543 AN: 10578

Middle Eastern (MID) AF: 0.456 AC: 134 AN: 294

European-Non Finnish (NFE) AF: 0.535 AC: 36386 AN: 67954

Other (OTH) AF: 0.481 AC: 1017 AN: 2114

Alfa AF: 0.515 Hom.: 46416

Bravo AF: 0.499

Asia WGS AF: 0.693 AC: 2405 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	12
DANN	Benign	0.84
PhyloP100		0.68

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1361600;

hg19: chr1-95007918;