rs10503951

Variant names:

• chr8-33808162-A-G
• rs10503951
• ENST00000521541.2:n.313+11726A>G

Variant summary

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

The ENST00000521541.2(ENSG00000253642):​n.313+11726A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0646 in 152,298 control chromosomes in the GnomAD database, including 524 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 0.065 (524 hom., cov: 32)
• Consequence: ENSG00000253642 ENST00000521541.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.08
• Publications: 9 publications found

Genes affected

ENSG00000253642 (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 = 0.239 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000521541.2. 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
	LOC105379364	NR_189605.1		n.745+11726A>G		intron	N/A
	LOC105379364	NR_189606.1		n.330+11726A>G		intron	N/A
	LOC105379364	NR_189607.1		n.330+11726A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000253642	ENST00000521541.2	TSL:2	n.313+11726A>G		intron	N/A
	ENSG00000253642	ENST00000523063.5	TSL:3	n.504+11726A>G		intron	N/A
	ENSG00000253642	ENST00000523336.2	TSL:2	n.147+11726A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0646 AC: 9837 AN: 152180 Hom.: 523 Cov.: 32

Gnomad AFR AF: 0.0167

Gnomad AMI AF: 0.0603

Gnomad AMR AF: 0.0511

Gnomad ASJ AF: 0.0510

Gnomad EAS AF: 0.249

Gnomad SAS AF: 0.0871

Gnomad FIN AF: 0.0852

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0790

Gnomad OTH AF: 0.0606

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

GnomAD4 genome AF: 0.0646 AC: 9844 AN: 152298 Hom.: 524 Cov.: 32 AF XY: 0.0662 AC XY: 4927 AN XY: 74474

African (AFR) AF: 0.0166 AC: 692 AN: 41576

American (AMR) AF: 0.0512 AC: 783 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0510 AC: 177 AN: 3472

East Asian (EAS) AF: 0.250 AC: 1294 AN: 5178

South Asian (SAS) AF: 0.0878 AC: 424 AN: 4828

European-Finnish (FIN) AF: 0.0852 AC: 905 AN: 10622

Middle Eastern (MID) AF: 0.0374 AC: 11 AN: 294

European-Non Finnish (NFE) AF: 0.0790 AC: 5375 AN: 68012

Other (OTH) AF: 0.0605 AC: 128 AN: 2116

Alfa AF: 0.0758 Hom.: 1660

Bravo AF: 0.0602

Asia WGS AF: 0.148 AC: 514 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.2
DANN	Benign	0.72
PhyloP100		1.1

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: rs10503951;

hg19: chr8-33665680;