10-73886124-G-T

Variant names:

• chr10-73886124-G-T
• rs2633303
• ENST00000746715.1:n.688+2143C>A

Variant summary

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

The ENST00000746715.1(ENSG00000297271):​n.688+2143C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.725 in 152,024 control chromosomes in the GnomAD database, including 40,685 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 0.73 (40685 hom., cov: 31)
• Consequence: ENSG00000297271 ENST00000746715.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.332
• Publications: 3 publications found

Genes affected

ENSG00000297271 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.766 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
ENSG00000297271	ENST00000746715.1	n.688+2143C>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.725 AC: 110194 AN: 151908 Hom.: 40652 Cov.: 31

Gnomad AFR AF: 0.773

Gnomad AMI AF: 0.687

Gnomad AMR AF: 0.598

Gnomad ASJ AF: 0.907

Gnomad EAS AF: 0.481

Gnomad SAS AF: 0.604

Gnomad FIN AF: 0.630

Gnomad MID AF: 0.861

Gnomad NFE AF: 0.756

Gnomad OTH AF: 0.777

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

GnomAD4 genome AF: 0.725 AC: 110262 AN: 152024 Hom.: 40685 Cov.: 31 AF XY: 0.716 AC XY: 53176 AN XY: 74312

African (AFR) AF: 0.773 AC: 32068 AN: 41488

American (AMR) AF: 0.597 AC: 9116 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.907 AC: 3149 AN: 3472

East Asian (EAS) AF: 0.481 AC: 2485 AN: 5164

South Asian (SAS) AF: 0.604 AC: 2906 AN: 4814

European-Finnish (FIN) AF: 0.630 AC: 6646 AN: 10552

Middle Eastern (MID) AF: 0.867 AC: 255 AN: 294

European-Non Finnish (NFE) AF: 0.756 AC: 51390 AN: 67964

Other (OTH) AF: 0.769 AC: 1622 AN: 2108

Alfa AF: 0.708 Hom.: 4870

Bravo AF: 0.726

Asia WGS AF: 0.523 AC: 1824 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	2.3
DANN	Benign	0.47
PhyloP100		-0.33

Splicing

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

Other links and lift over

dbSNP: rs2633303; hg19: chr10-75645882;