rs4933466

Variant names:

• chr10-88089762-A-G
• rs4933466
• ENST00000752267.1:n.648+28332A>G

Your query was ambiguous. Multiple possible variants found:

• chr10-88089762-A-G
• chr10-88089762-A-T

Variant summary

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

The ENST00000752267.1(ENSG00000297977):​n.648+28332A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.356 in 152,222 control chromosomes in the GnomAD database, including 10,898 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 0.36 (10898 hom., cov: 33)
• Consequence: ENSG00000297977 ENST00000752267.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.932
• Publications: 5 publications found

Genes affected

ENSG00000297977 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.752 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105378415	XR_007062225.1	n.82-20T>C		intron_variant	Intron 1 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000297977	ENST00000752267.1	n.648+28332A>G		intron_variant	Intron 4 of 4
ENSG00000297977	ENST00000752268.1	n.674+20120A>G		intron_variant	Intron 5 of 5
ENSG00000297977	ENST00000752271.1	n.262+22909A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.357 AC: 54239 AN: 152104 Hom.: 10893 Cov.: 33

Gnomad AFR AF: 0.189

Gnomad AMI AF: 0.338

Gnomad AMR AF: 0.414

Gnomad ASJ AF: 0.439

Gnomad EAS AF: 0.771

Gnomad SAS AF: 0.400

Gnomad FIN AF: 0.420

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.398

Gnomad OTH AF: 0.357

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

GnomAD4 genome AF: 0.356 AC: 54260 AN: 152222 Hom.: 10898 Cov.: 33 AF XY: 0.363 AC XY: 27045 AN XY: 74414

African (AFR) AF: 0.189 AC: 7837 AN: 41562

American (AMR) AF: 0.414 AC: 6338 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.439 AC: 1521 AN: 3468

East Asian (EAS) AF: 0.772 AC: 4004 AN: 5186

South Asian (SAS) AF: 0.400 AC: 1930 AN: 4828

European-Finnish (FIN) AF: 0.420 AC: 4447 AN: 10582

Middle Eastern (MID) AF: 0.276 AC: 81 AN: 294

European-Non Finnish (NFE) AF: 0.398 AC: 27040 AN: 67986

Other (OTH) AF: 0.357 AC: 754 AN: 2112

Alfa AF: 0.380 Hom.: 19270

Bravo AF: 0.350

Asia WGS AF: 0.540 AC: 1878 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.13
DANN	Benign	0.48
PhyloP100		-0.93

Splicing

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

Other links and lift over

dbSNP: rs4933466; hg19: chr10-89849519;