ENST00000797104.1:n.144-2190C>T

Variant names:

• chr2-223589234-G-A
• rs959100
• ENST00000797104.1:n.144-2190C>T

Variant summary

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

The ENST00000797104.1(ENSG00000303770):​n.144-2190C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.173 in 152,106 control chromosomes in the GnomAD database, including 2,553 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 0.17 (2553 hom., cov: 32)
• Consequence: ENSG00000303770 ENST00000797104.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.365
• Publications: 1 publications found

Genes affected

ENSG00000303770 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.218 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
ENSG00000303770	ENST00000797104.1	n.144-2190C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.173 AC: 26349 AN: 151988 Hom.: 2551 Cov.: 32

Gnomad AFR AF: 0.109

Gnomad AMI AF: 0.441

Gnomad AMR AF: 0.173

Gnomad ASJ AF: 0.275

Gnomad EAS AF: 0.0772

Gnomad SAS AF: 0.127

Gnomad FIN AF: 0.125

Gnomad MID AF: 0.264

Gnomad NFE AF: 0.221

Gnomad OTH AF: 0.190

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

GnomAD4 genome AF: 0.173 AC: 26352 AN: 152106 Hom.: 2553 Cov.: 32 AF XY: 0.167 AC XY: 12420 AN XY: 74360

African (AFR) AF: 0.109 AC: 4517 AN: 41482

American (AMR) AF: 0.173 AC: 2645 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.275 AC: 955 AN: 3472

East Asian (EAS) AF: 0.0772 AC: 399 AN: 5170

South Asian (SAS) AF: 0.126 AC: 608 AN: 4824

European-Finnish (FIN) AF: 0.125 AC: 1320 AN: 10572

Middle Eastern (MID) AF: 0.253 AC: 74 AN: 292

European-Non Finnish (NFE) AF: 0.221 AC: 15030 AN: 67988

Other (OTH) AF: 0.191 AC: 403 AN: 2114

Alfa AF: 0.216 Hom.: 3070

Bravo AF: 0.173

Asia WGS AF: 0.109 AC: 381 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	3.5
DANN	Benign	0.28
PhyloP100		0.36

Splicing

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

Other links and lift over

dbSNP: rs959100; hg19: chr2-224453952;