1-90410331-T-C

Variant names:

• chr1-90410331-T-C
• rs2136093
• ENST00000653744.1:n.171-9204A>G

Variant summary

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

The ENST00000653744.1(ENSG00000287372):​n.171-9204A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.601 in 152,008 control chromosomes in the GnomAD database, including 28,767 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 0.60 (28767 hom., cov: 33)
• Consequence: ENSG00000287372 ENST00000653744.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.243
• Publications: 10 publications found

Genes affected

ENSG00000287372 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.699 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
ENSG00000287372	ENST00000653744.1	n.171-9204A>G		intron_variant	Intron 1 of 2
ENSG00000287372	ENST00000655087.1	n.420-9204A>G		intron_variant	Intron 1 of 1
ENSG00000299349	ENST00000762792.1	n.158+25220T>C		intron_variant	Intron 2 of 2
ENSG00000287372	ENST00000762859.1	n.108+9647A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.601 AC: 91260 AN: 151890 Hom.: 28764 Cov.: 33

Gnomad AFR AF: 0.449

Gnomad AMI AF: 0.802

Gnomad AMR AF: 0.663

Gnomad ASJ AF: 0.624

Gnomad EAS AF: 0.213

Gnomad SAS AF: 0.552

Gnomad FIN AF: 0.615

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.704

Gnomad OTH AF: 0.644

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

GnomAD4 genome AF: 0.601 AC: 91284 AN: 152008 Hom.: 28767 Cov.: 33 AF XY: 0.595 AC XY: 44219 AN XY: 74304

African (AFR) AF: 0.449 AC: 18608 AN: 41460

American (AMR) AF: 0.663 AC: 10113 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.624 AC: 2165 AN: 3468

East Asian (EAS) AF: 0.213 AC: 1099 AN: 5156

South Asian (SAS) AF: 0.551 AC: 2660 AN: 4826

European-Finnish (FIN) AF: 0.615 AC: 6509 AN: 10586

Middle Eastern (MID) AF: 0.646 AC: 190 AN: 294

European-Non Finnish (NFE) AF: 0.704 AC: 47861 AN: 67946

Other (OTH) AF: 0.638 AC: 1348 AN: 2112

Alfa AF: 0.640 Hom.: 37682

Bravo AF: 0.598

Asia WGS AF: 0.413 AC: 1444 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	6.5
DANN	Benign	0.75
PhyloP100		0.24

Splicing

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

Other links and lift over

dbSNP: rs2136093; hg19: chr1-90875888;