rs9544495

Variant names:

• chr13-77423278-A-C
• rs9544495
• ENST00000783824.1:n.256+4488A>C

Variant summary

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

The ENST00000783824.1(ENSG00000285714):​n.256+4488A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.49 in 152,144 control chromosomes in the GnomAD database, including 21,672 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 0.49 (21672 hom., cov: 33)
• Consequence: ENSG00000285714 ENST00000783824.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.327
• Publications: 1 publications found

Genes affected

ENSG00000285714 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.667 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124903185	XM_047430828.1	c.*340A>C		downstream_gene_variant			XP_047286784.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000285714	ENST00000783824.1	n.256+4488A>C		intron_variant	Intron 2 of 2
ENSG00000285714	ENST00000649088.2	n.*172A>C		downstream_gene_variant
ENSG00000285714	ENST00000783822.1	n.*172A>C		downstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.491 AC: 74578 AN: 152026 Hom.: 21680 Cov.: 33

Gnomad AFR AF: 0.184

Gnomad AMI AF: 0.607

Gnomad AMR AF: 0.462

Gnomad ASJ AF: 0.632

Gnomad EAS AF: 0.268

Gnomad SAS AF: 0.465

Gnomad FIN AF: 0.624

Gnomad MID AF: 0.566

Gnomad NFE AF: 0.672

Gnomad OTH AF: 0.511

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

GnomAD4 genome AF: 0.490 AC: 74570 AN: 152144 Hom.: 21672 Cov.: 33 AF XY: 0.485 AC XY: 36073 AN XY: 74358

African (AFR) AF: 0.184 AC: 7630 AN: 41530

American (AMR) AF: 0.461 AC: 7053 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.632 AC: 2188 AN: 3462

East Asian (EAS) AF: 0.267 AC: 1384 AN: 5174

South Asian (SAS) AF: 0.465 AC: 2243 AN: 4820

European-Finnish (FIN) AF: 0.624 AC: 6592 AN: 10572

Middle Eastern (MID) AF: 0.575 AC: 169 AN: 294

European-Non Finnish (NFE) AF: 0.672 AC: 45683 AN: 67988

Other (OTH) AF: 0.510 AC: 1076 AN: 2110

Alfa AF: 0.604 Hom.: 14087

Bravo AF: 0.463

Asia WGS AF: 0.361 AC: 1254 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.53
DANN	Benign	0.59
PhyloP100		-0.33

Splicing

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

Other links and lift over

dbSNP: rs9544495; hg19: chr13-77997413;