rs4529792

Positions:

• chr10-64182569-C-A
• chr10-64182569-C-G
• chr10-64182569-C-T

Variant summary

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

The ENST00000654191.1(ENSG00000228566):​n.597-118947C>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 0.666 in 152,124 control chromosomes in the GnomAD database, including 40,442 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 0.67 (40442 hom., cov: 33)
• Consequence: ENST00000654191.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.424

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.861 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124902439	XR_007062161.1	n.578-118947C>A		intron_variant, non_coding_transcript_variant
LOC124902439	XR_007062160.1	n.576-118947C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000654191.1	n.597-118947C>A		intron_variant, non_coding_transcript_variant
	ENST00000660795.1	n.346-118947C>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.667 AC: 101328 AN: 152006 Hom.: 40442 Cov.: 33

Gnomad AFR AF: 0.192

Gnomad AMI AF: 0.912

Gnomad AMR AF: 0.761

Gnomad ASJ AF: 0.882

Gnomad EAS AF: 0.844

Gnomad SAS AF: 0.798

Gnomad FIN AF: 0.844

Gnomad MID AF: 0.813

Gnomad NFE AF: 0.867

Gnomad OTH AF: 0.704

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

GnomAD4 genome AF: 0.666 AC: 101331 AN: 152124 Hom.: 40442 Cov.: 33 AF XY: 0.672 AC XY: 49986 AN XY: 74382

Gnomad4 AFR AF: 0.191

Gnomad4 AMR AF: 0.761

Gnomad4 ASJ AF: 0.882

Gnomad4 EAS AF: 0.845

Gnomad4 SAS AF: 0.798

Gnomad4 FIN AF: 0.844

Gnomad4 NFE AF: 0.867

Gnomad4 OTH AF: 0.704

Alfa AF: 0.806 Hom.: 12087

Bravo AF: 0.638

Asia WGS AF: 0.783 AC: 2706 AN: 3456

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.4
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: rs4529792; hg19: chr10-65942330;