rs10515859

Positions:

• chr5-163417562-G-C

Variant summary

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

The ENST00000646617.1(ENSG00000254186):​n.322+8241C>G 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 0.426 in 152,012 control chromosomes in the GnomAD database, including 14,250 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 0.43 (14250 hom., cov: 32)
• Consequence: ENST00000646617.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.27

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.463 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105377700	XR_001742962.3	n.141-5179C>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000646617.1	n.322+8241C>G		intron_variant, non_coding_transcript_variant
	ENST00000503504.1	n.355+8241C>G		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.426 AC: 64781 AN: 151894 Hom.: 14240 Cov.: 32

Gnomad AFR AF: 0.436

Gnomad AMI AF: 0.434

Gnomad AMR AF: 0.428

Gnomad ASJ AF: 0.399

Gnomad EAS AF: 0.0594

Gnomad SAS AF: 0.233

Gnomad FIN AF: 0.401

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.467

Gnomad OTH AF: 0.439

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

GnomAD4 genome AF: 0.426 AC: 64816 AN: 152012 Hom.: 14250 Cov.: 32 AF XY: 0.418 AC XY: 31100 AN XY: 74340

Gnomad4 AFR AF: 0.435

Gnomad4 AMR AF: 0.427

Gnomad4 ASJ AF: 0.399

Gnomad4 EAS AF: 0.0597

Gnomad4 SAS AF: 0.234

Gnomad4 FIN AF: 0.401

Gnomad4 NFE AF: 0.467

Gnomad4 OTH AF: 0.434

Alfa AF: 0.456 Hom.: 2018

Bravo AF: 0.430

Asia WGS AF: 0.201 AC: 702 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.086
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10515859; hg19: chr5-162844568;