rs10050871

Variant names:

• chr5-163380371-G-A
• rs10050871
• ENST00000503504.2:n.375+45432C>T

Variant summary

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

The ENST00000509211.2(ENSG00000254186):​n.390+31948C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.35 in 152,006 control chromosomes in the GnomAD database, including 10,055 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 0.35 (10055 hom., cov: 32)
• Consequence: ENSG00000254186 ENST00000509211.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.55
• Publications: 1 publications found

Genes affected

ENSG00000254186 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.44 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000509211.2. 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
	ENSG00000254186	ENST00000503504.2	TSL:5	n.375+45432C>T		intron	N/A
	ENSG00000254186	ENST00000503615.6	TSL:5	n.351+45432C>T		intron	N/A
	ENSG00000254186	ENST00000509211.2	TSL:3	n.390+31948C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.350 AC: 53203 AN: 151886 Hom.: 10056 Cov.: 32

Gnomad AFR AF: 0.271

Gnomad AMI AF: 0.431

Gnomad AMR AF: 0.292

Gnomad ASJ AF: 0.383

Gnomad EAS AF: 0.0511

Gnomad SAS AF: 0.229

Gnomad FIN AF: 0.326

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.444

Gnomad OTH AF: 0.368

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

GnomAD4 genome AF: 0.350 AC: 53204 AN: 152006 Hom.: 10055 Cov.: 32 AF XY: 0.338 AC XY: 25143 AN XY: 74300

African (AFR) AF: 0.270 AC: 11210 AN: 41478

American (AMR) AF: 0.291 AC: 4445 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.383 AC: 1329 AN: 3472

East Asian (EAS) AF: 0.0516 AC: 267 AN: 5174

South Asian (SAS) AF: 0.229 AC: 1102 AN: 4820

European-Finnish (FIN) AF: 0.326 AC: 3437 AN: 10554

Middle Eastern (MID) AF: 0.364 AC: 107 AN: 294

European-Non Finnish (NFE) AF: 0.444 AC: 30147 AN: 67924

Other (OTH) AF: 0.364 AC: 769 AN: 2112

Alfa AF: 0.404 Hom.: 1646

Bravo AF: 0.343

Asia WGS AF: 0.177 AC: 619 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.99
DANN	Benign	0.32
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: rs10050871;

hg19: chr5-162807377;