rs10500517

Positions:

• chr16-65271607-C-A

Variant summary

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

The ENST00000562656.1(ENSG00000260364):​n.271+19738C>A 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 0.0359 in 152,196 control chromosomes in the GnomAD database, including 141 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 0.036 (141 hom., cov: 32)
• Consequence: ENST00000562656.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.124

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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 = 0.0898 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124903780	XR_007065224.1	n.1283+19738C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000562656.1	n.271+19738C>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.0358 AC: 5452 AN: 152078 Hom.: 142 Cov.: 32

Gnomad AFR AF: 0.0632

Gnomad AMI AF: 0.0219

Gnomad AMR AF: 0.0206

Gnomad ASJ AF: 0.0242

Gnomad EAS AF: 0.0969

Gnomad SAS AF: 0.0182

Gnomad FIN AF: 0.00990

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0243

Gnomad OTH AF: 0.0282

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

GnomAD4 genome AF: 0.0359 AC: 5466 AN: 152196 Hom.: 141 Cov.: 32 AF XY: 0.0349 AC XY: 2601 AN XY: 74436

Gnomad4 AFR AF: 0.0633

Gnomad4 AMR AF: 0.0206

Gnomad4 ASJ AF: 0.0242

Gnomad4 EAS AF: 0.0968

Gnomad4 SAS AF: 0.0184

Gnomad4 FIN AF: 0.00990

Gnomad4 NFE AF: 0.0243

Gnomad4 OTH AF: 0.0289

Alfa AF: 0.0247 Hom.: 54

Bravo AF: 0.0376

Asia WGS AF: 0.0620 AC: 218 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.74
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10500517; hg19: chr16-65305510;