rs491996

Variant names:

• chr15-47886049-T-A
• rs491996
• ENST00000560900.1:n.195+1545T>A

Your query was ambiguous. Multiple possible variants found:

• chr15-47886049-T-A
• chr15-47886049-T-C
• chr15-47886049-T-G

Variant summary

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

The ENST00000560900.1(ENSG00000259754):​n.195+1545T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.128 in 152,088 control chromosomes in the GnomAD database, including 1,761 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 0.13 (1761 hom., cov: 32)
• Consequence: ENSG00000259754 ENST00000560900.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.532
• 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=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.332 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+1545T>A		intron	N/A
	ENSG00000259754	ENST00000662551.1		n.188+73133T>A		intron	N/A
	ENSG00000259754	ENST00000664705.1		n.188+73133T>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.127 AC: 19363 AN: 151970 Hom.: 1750 Cov.: 32

Gnomad AFR AF: 0.192

Gnomad AMI AF: 0.182

Gnomad AMR AF: 0.160

Gnomad ASJ AF: 0.0360

Gnomad EAS AF: 0.346

Gnomad SAS AF: 0.276

Gnomad FIN AF: 0.0709

Gnomad MID AF: 0.0573

Gnomad NFE AF: 0.0674

Gnomad OTH AF: 0.104

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

GnomAD4 genome AF: 0.128 AC: 19415 AN: 152088 Hom.: 1761 Cov.: 32 AF XY: 0.131 AC XY: 9740 AN XY: 74350

African (AFR) AF: 0.193 AC: 7984 AN: 41464

American (AMR) AF: 0.161 AC: 2454 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0360 AC: 125 AN: 3470

East Asian (EAS) AF: 0.346 AC: 1786 AN: 5166

South Asian (SAS) AF: 0.275 AC: 1326 AN: 4816

European-Finnish (FIN) AF: 0.0709 AC: 751 AN: 10586

Middle Eastern (MID) AF: 0.0411 AC: 12 AN: 292

European-Non Finnish (NFE) AF: 0.0674 AC: 4579 AN: 67988

Other (OTH) AF: 0.110 AC: 232 AN: 2112

Alfa AF: 0.0394 Hom.: 39

Bravo AF: 0.134

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	0.23
DANN	Benign	0.60
PhyloP100		-0.53

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: rs491996;

hg19: chr15-48178246;