rs10050871

chr5-163380371-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000646617.1(ENSG00000254186):n.322+45432C>T variant causes a intron, non coding transcript 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: ENST00000646617.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.55

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105377700	XR_001742961.2	n.1236+31948C>T		intron_variant, non_coding_transcript_variant
LOC105377700	XR_001742965.1	n.1236+31948C>T		intron_variant, non_coding_transcript_variant
LOC105377700	XR_002956233.2	n.1236+31948C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000646617.1	n.322+45432C>T		intron_variant, non_coding_transcript_variant
	ENST00000503504.1	n.355+45432C>T		intron_variant, non_coding_transcript_variant		5

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

Gnomad4 AFR AF: 0.270

Gnomad4 AMR AF: 0.291

Gnomad4 ASJ AF: 0.383

Gnomad4 EAS AF: 0.0516

Gnomad4 SAS AF: 0.229

Gnomad4 FIN AF: 0.326

Gnomad4 NFE AF: 0.444

Gnomad4 OTH AF: 0.364

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	0.99
Dann	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10050871; hg19: chr5-162807377;