1-36639676-T-C

Variant names:

• chr1-36639676-T-C
• rs10908312
• ENST00000722329.1:n.440-5544T>C

Variant summary

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

The ENST00000722329.1(ENSG00000294271):​n.440-5544T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.574 in 152,198 control chromosomes in the GnomAD database, including 29,118 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 0.57 (29118 hom., cov: 33)
• Consequence: ENSG00000294271 ENST00000722329.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.482
• Publications: 2 publications found

Genes affected

ENSG00000294271 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.893 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
ENSG00000294271	ENST00000722329.1	n.440-5544T>C		intron_variant	Intron 2 of 2
ENSG00000294271	ENST00000722330.1	n.569+3431T>C		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.574 AC: 87310 AN: 152080 Hom.: 29054 Cov.: 33

Gnomad AFR AF: 0.885

Gnomad AMI AF: 0.338

Gnomad AMR AF: 0.632

Gnomad ASJ AF: 0.417

Gnomad EAS AF: 0.915

Gnomad SAS AF: 0.633

Gnomad FIN AF: 0.402

Gnomad MID AF: 0.547

Gnomad NFE AF: 0.379

Gnomad OTH AF: 0.579

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

GnomAD4 genome AF: 0.574 AC: 87430 AN: 152198 Hom.: 29118 Cov.: 33 AF XY: 0.579 AC XY: 43077 AN XY: 74410

African (AFR) AF: 0.885 AC: 36786 AN: 41556

American (AMR) AF: 0.633 AC: 9664 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.417 AC: 1447 AN: 3470

East Asian (EAS) AF: 0.915 AC: 4741 AN: 5184

South Asian (SAS) AF: 0.631 AC: 3043 AN: 4820

European-Finnish (FIN) AF: 0.402 AC: 4252 AN: 10584

Middle Eastern (MID) AF: 0.541 AC: 159 AN: 294

European-Non Finnish (NFE) AF: 0.379 AC: 25796 AN: 67990

Other (OTH) AF: 0.584 AC: 1234 AN: 2114

Alfa AF: 0.341 Hom.: 1359

Bravo AF: 0.608

Asia WGS AF: 0.800 AC: 2780 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.2
DANN	Benign	0.37
PhyloP100		-0.48

Splicing

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

Other links and lift over

dbSNP: rs10908312; hg19: chr1-37105277;