rs224123

Variant names:

• chr10-62691473-C-T
• rs224123
• ENST00000649548.2:n.160-5394G>A

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000649548.2(ENSG00000238280):​n.160-5394G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.679 in 152,132 control chromosomes in the GnomAD database, including 37,019 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 0.68 (37019 hom., cov: 32)
• Consequence: ENSG00000238280 ENST00000649548.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.62
• Publications: 6 publications found

Genes affected

ENSG00000238280 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.45).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.917 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000649548.2. 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
	ENSG00000238280	ENST00000649548.2		n.160-5394G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.679 AC: 103156 AN: 152014 Hom.: 36949 Cov.: 32

Gnomad AFR AF: 0.925

Gnomad AMI AF: 0.562

Gnomad AMR AF: 0.587

Gnomad ASJ AF: 0.523

Gnomad EAS AF: 0.441

Gnomad SAS AF: 0.683

Gnomad FIN AF: 0.577

Gnomad MID AF: 0.639

Gnomad NFE AF: 0.593

Gnomad OTH AF: 0.636

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

GnomAD4 genome AF: 0.679 AC: 103288 AN: 152132 Hom.: 37019 Cov.: 32 AF XY: 0.675 AC XY: 50213 AN XY: 74362

African (AFR) AF: 0.925 AC: 38451 AN: 41560

American (AMR) AF: 0.587 AC: 8980 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.523 AC: 1816 AN: 3470

East Asian (EAS) AF: 0.440 AC: 2277 AN: 5174

South Asian (SAS) AF: 0.683 AC: 3290 AN: 4814

European-Finnish (FIN) AF: 0.577 AC: 6085 AN: 10546

Middle Eastern (MID) AF: 0.653 AC: 192 AN: 294

European-Non Finnish (NFE) AF: 0.593 AC: 40330 AN: 67970

Other (OTH) AF: 0.643 AC: 1357 AN: 2110

Alfa AF: 0.608 Hom.: 12286

Bravo AF: 0.685

Asia WGS AF: 0.640 AC: 2227 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.45
CADD	Benign	15
DANN	Benign	0.55
PhyloP100		1.6

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: rs224123;

hg19: chr10-64451233;