rs4886887

Positions:

• chr15-77605861-C-T

Variant summary

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

The ENST00000561123.2(ENSG00000259420):​n.578-2679C>T 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 0.212 in 152,156 control chromosomes in the GnomAD database, including 3,600 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 0.21 (3600 hom., cov: 33)
• Consequence: ENST00000561123.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.15

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.246 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105370906	XR_001751806.2	n.689-24424C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000561123.2	n.578-2679C>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.212 AC: 32209 AN: 152038 Hom.: 3602 Cov.: 33

Gnomad AFR AF: 0.149

Gnomad AMI AF: 0.259

Gnomad AMR AF: 0.239

Gnomad ASJ AF: 0.178

Gnomad EAS AF: 0.189

Gnomad SAS AF: 0.194

Gnomad FIN AF: 0.204

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.249

Gnomad OTH AF: 0.219

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

GnomAD4 genome AF: 0.212 AC: 32206 AN: 152156 Hom.: 3600 Cov.: 33 AF XY: 0.208 AC XY: 15489 AN XY: 74392

Gnomad4 AFR AF: 0.148

Gnomad4 AMR AF: 0.239

Gnomad4 ASJ AF: 0.178

Gnomad4 EAS AF: 0.189

Gnomad4 SAS AF: 0.193

Gnomad4 FIN AF: 0.204

Gnomad4 NFE AF: 0.249

Gnomad4 OTH AF: 0.217

Alfa AF: 0.230 Hom.: 524

Bravo AF: 0.212

Asia WGS AF: 0.179 AC: 624 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.45
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4886887; hg19: chr15-77898203;