rs10518517

chr4-127216057-A-G

Variant summary

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

The ENST00000504050.5(ENSG00000248491):n.369-21564T>C 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 0.0252 in 152,284 control chromosomes in the GnomAD database, including 324 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 0.025 (324 hom., cov: 33)
• Consequence: ENST00000504050.5 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.47

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.293 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC102724210	XR_001741824.3	n.372-21564T>C		intron_variant, non_coding_transcript_variant
LOC102724210	XR_001741825.2	n.124-21564T>C		intron_variant, non_coding_transcript_variant
LOC102724210	XR_939184.4	n.124-109283T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000504050.5	n.369-21564T>C		intron_variant, non_coding_transcript_variant		5
	ENST00000661442.1	n.364-21564T>C		intron_variant, non_coding_transcript_variant
	ENST00000667124.1	n.237-21564T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0252 AC: 3836 AN: 152166 Hom.: 327 Cov.: 33

Gnomad AFR AF: 0.00591

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0795

Gnomad ASJ AF: 0.00288

Gnomad EAS AF: 0.307

Gnomad SAS AF: 0.0186

Gnomad FIN AF: 0.0176

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.00665

Gnomad OTH AF: 0.0225

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

GnomAD4 genome AF: 0.0252 AC: 3834 AN: 152284 Hom.: 324 Cov.: 33 AF XY: 0.0285 AC XY: 2124 AN XY: 74466

Gnomad4 AFR AF: 0.00589

Gnomad4 AMR AF: 0.0796

Gnomad4 ASJ AF: 0.00288

Gnomad4 EAS AF: 0.306

Gnomad4 SAS AF: 0.0192

Gnomad4 FIN AF: 0.0176

Gnomad4 NFE AF: 0.00665

Gnomad4 OTH AF: 0.0213

Alfa AF: 0.0130 Hom.: 14

Bravo AF: 0.0294

Asia WGS AF: 0.147 AC: 508 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	0.022
Dann	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10518517; hg19: chr4-128137212;