rs224731

Variant names:

• chr10-33937381-G-A
• rs224731
• ENST00000816303.1:n.825+1255C>T

Variant summary

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

The ENST00000816303.1(ENSG00000306217):​n.825+1255C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.751 in 152,042 control chromosomes in the GnomAD database, including 43,602 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 0.75 (43602 hom., cov: 32)
• Consequence: ENSG00000306217 ENST00000816303.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.105
• Publications: 1 publications found

Genes affected

ENSG00000306217 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.48).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.904 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000816303.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000306217	ENST00000816303.1		n.825+1255C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.751 AC: 114047 AN: 151924 Hom.: 43553 Cov.: 32

Gnomad AFR AF: 0.912

Gnomad AMI AF: 0.734

Gnomad AMR AF: 0.636

Gnomad ASJ AF: 0.644

Gnomad EAS AF: 0.756

Gnomad SAS AF: 0.754

Gnomad FIN AF: 0.695

Gnomad MID AF: 0.725

Gnomad NFE AF: 0.693

Gnomad OTH AF: 0.717

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

GnomAD4 genome AF: 0.751 AC: 114147 AN: 152042 Hom.: 43602 Cov.: 32 AF XY: 0.749 AC XY: 55616 AN XY: 74302

African (AFR) AF: 0.912 AC: 37848 AN: 41514

American (AMR) AF: 0.635 AC: 9693 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.644 AC: 2232 AN: 3468

East Asian (EAS) AF: 0.756 AC: 3893 AN: 5148

South Asian (SAS) AF: 0.753 AC: 3630 AN: 4818

European-Finnish (FIN) AF: 0.695 AC: 7330 AN: 10550

Middle Eastern (MID) AF: 0.728 AC: 214 AN: 294

European-Non Finnish (NFE) AF: 0.693 AC: 47129 AN: 67968

Other (OTH) AF: 0.715 AC: 1510 AN: 2112

Alfa AF: 0.701 Hom.: 57739

Bravo AF: 0.751

Asia WGS AF: 0.716 AC: 2490 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.48
CADD	Benign	5.2
DANN	Benign	0.80
PhyloP100		-0.10

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs224731;

hg19: chr10-34226309;