rs6533015

Positions:

• chr4-102434376-C-G
• chr4-102434376-C-T

Variant summary

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

The NR_136202.1(LOC105377621):​n.186-14582G>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 0.631 in 151,866 control chromosomes in the GnomAD database, including 31,105 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 0.63 (31105 hom., cov: 31)
• Consequence: LOC105377621 NR_136202.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.263

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.772 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105377621	NR_136202.1	n.186-14582G>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000512915.5	n.81-14582G>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.630 AC: 95674 AN: 151748 Hom.: 31051 Cov.: 31

Gnomad AFR AF: 0.779

Gnomad AMI AF: 0.595

Gnomad AMR AF: 0.530

Gnomad ASJ AF: 0.656

Gnomad EAS AF: 0.367

Gnomad SAS AF: 0.631

Gnomad FIN AF: 0.586

Gnomad MID AF: 0.712

Gnomad NFE AF: 0.588

Gnomad OTH AF: 0.626

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

GnomAD4 genome AF: 0.631 AC: 95787 AN: 151866 Hom.: 31105 Cov.: 31 AF XY: 0.628 AC XY: 46638 AN XY: 74208

Gnomad4 AFR AF: 0.779

Gnomad4 AMR AF: 0.531

Gnomad4 ASJ AF: 0.656

Gnomad4 EAS AF: 0.366

Gnomad4 SAS AF: 0.631

Gnomad4 FIN AF: 0.586

Gnomad4 NFE AF: 0.588

Gnomad4 OTH AF: 0.628

Alfa AF: 0.606 Hom.: 3376

Bravo AF: 0.632

Asia WGS AF: 0.496 AC: 1724 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.1
DANN	Benign	0.24

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6533015; hg19: chr4-103355533;