rs9536919

Variant names:

• chr13-54949643-A-G
• rs9536919
• XM_047430847.1:c.161-2658A>G

Your query was ambiguous. Multiple possible variants found:

• chr13-54949643-A-G
• chr13-54949643-A-T

Variant summary

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

The ENST00000616396.2(ENSG00000277047):​n.166-2658A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.703 in 152,090 control chromosomes in the GnomAD database, including 38,814 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 0.70 (38814 hom., cov: 33)
• Consequence: ENSG00000277047 ENST00000616396.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.451
• Publications: 2 publications found

Genes affected

LOC124903233 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.796 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000616396.2. 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
	ENSG00000277047	ENST00000616396.2	TSL:3	n.166-2658A>G		intron	N/A
	ENSG00000277047	ENST00000622486.5	TSL:3	n.169-2658A>G		intron	N/A
	ENSG00000277047	ENST00000653085.1		n.172-2658A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.703 AC: 106882 AN: 151972 Hom.: 38806 Cov.: 33

Gnomad AFR AF: 0.512

Gnomad AMI AF: 0.675

Gnomad AMR AF: 0.753

Gnomad ASJ AF: 0.817

Gnomad EAS AF: 0.642

Gnomad SAS AF: 0.695

Gnomad FIN AF: 0.738

Gnomad MID AF: 0.775

Gnomad NFE AF: 0.802

Gnomad OTH AF: 0.728

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

GnomAD4 genome AF: 0.703 AC: 106923 AN: 152090 Hom.: 38814 Cov.: 33 AF XY: 0.701 AC XY: 52109 AN XY: 74352

African (AFR) AF: 0.512 AC: 21233 AN: 41466

American (AMR) AF: 0.753 AC: 11505 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.817 AC: 2836 AN: 3470

East Asian (EAS) AF: 0.642 AC: 3318 AN: 5168

South Asian (SAS) AF: 0.696 AC: 3357 AN: 4826

European-Finnish (FIN) AF: 0.738 AC: 7808 AN: 10576

Middle Eastern (MID) AF: 0.786 AC: 231 AN: 294

European-Non Finnish (NFE) AF: 0.802 AC: 54500 AN: 67994

Other (OTH) AF: 0.720 AC: 1523 AN: 2114

Alfa AF: 0.773 Hom.: 28226

Bravo AF: 0.695

Asia WGS AF: 0.612 AC: 2129 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	7.1
DANN	Benign	0.84
PhyloP100		0.45

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: rs9536919;

hg19: chr13-55523778;