15-47890556-G-C

Variant names:

• chr15-47890556-G-C
• rs677207
• ENST00000560900.1:n.195+6052G>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000560900.1(ENSG00000259754):​n.195+6052G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.115 in 152,022 control chromosomes in the GnomAD database, including 1,456 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 0.12 (1456 hom., cov: 31)
• Consequence: ENSG00000259754 ENST00000560900.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.397
• Publications: 0 publications found

Genes affected

ENSG00000259754 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.323 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000560900.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000259754	ENST00000560900.1	TSL:4	n.195+6052G>C		intron	N/A
	ENSG00000259754	ENST00000662551.1		n.188+77640G>C		intron	N/A
	ENSG00000259754	ENST00000664705.1		n.188+77640G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.115 AC: 17476 AN: 151904 Hom.: 1450 Cov.: 31

Gnomad AFR AF: 0.154

Gnomad AMI AF: 0.157

Gnomad AMR AF: 0.178

Gnomad ASJ AF: 0.0320

Gnomad EAS AF: 0.336

Gnomad SAS AF: 0.266

Gnomad FIN AF: 0.0677

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0619

Gnomad OTH AF: 0.100

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

GnomAD4 genome AF: 0.115 AC: 17521 AN: 152022 Hom.: 1456 Cov.: 31 AF XY: 0.119 AC XY: 8845 AN XY: 74318

African (AFR) AF: 0.154 AC: 6389 AN: 41460

American (AMR) AF: 0.178 AC: 2718 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.0320 AC: 111 AN: 3468

East Asian (EAS) AF: 0.336 AC: 1728 AN: 5146

South Asian (SAS) AF: 0.265 AC: 1273 AN: 4808

European-Finnish (FIN) AF: 0.0677 AC: 718 AN: 10602

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.0619 AC: 4208 AN: 67972

Other (OTH) AF: 0.106 AC: 223 AN: 2112

Alfa AF: 0.0366 Hom.: 31

Bravo AF: 0.124

Asia WGS AF: 0.331 AC: 1149 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	13
DANN	Benign	0.50
PhyloP100		0.40

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs677207;

hg19: chr15-48182753;