rs853803

Variant names:

• chr5-68466276-A-G
• rs853803
• ENST00000507733.3:n.347-31799T>C

Your query was ambiguous. Multiple possible variants found:

• chr5-68466276-A-G
• chr5-68466276-A-T

Variant summary

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

The ENST00000507733.3(ENSG00000248884):​n.347-31799T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.304 in 151,990 control chromosomes in the GnomAD database, including 7,410 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 0.30 (7410 hom., cov: 32)
• Consequence: ENSG00000248884 ENST00000507733.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.985
• Publications: 2 publications found

Genes affected

ENSG00000248884 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.478 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105379013	XR_007058804.1	n.474-32691T>C		intron_variant	Intron 3 of 4
LOC105379013	XR_007058805.1	n.144-32691T>C		intron_variant	Intron 2 of 3
LOC105379013	XR_007058806.1	n.2260-32691T>C		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000248884	ENST00000507733.3	n.347-31799T>C		intron_variant	Intron 3 of 5	2
ENSG00000248884	ENST00000701911.2	n.205-31799T>C		intron_variant	Intron 1 of 1
ENSG00000248884	ENST00000717704.1	n.144-9128T>C		intron_variant	Intron 2 of 6

Frequencies

GnomAD3 genomes AF: 0.303 AC: 46087 AN: 151872 Hom.: 7389 Cov.: 32

Gnomad AFR AF: 0.290

Gnomad AMI AF: 0.295

Gnomad AMR AF: 0.449

Gnomad ASJ AF: 0.299

Gnomad EAS AF: 0.493

Gnomad SAS AF: 0.332

Gnomad FIN AF: 0.241

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.272

Gnomad OTH AF: 0.313

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

GnomAD4 genome AF: 0.304 AC: 46143 AN: 151990 Hom.: 7410 Cov.: 32 AF XY: 0.309 AC XY: 22926 AN XY: 74284

African (AFR) AF: 0.290 AC: 12024 AN: 41430

American (AMR) AF: 0.450 AC: 6864 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.299 AC: 1037 AN: 3466

East Asian (EAS) AF: 0.494 AC: 2550 AN: 5164

South Asian (SAS) AF: 0.333 AC: 1600 AN: 4810

European-Finnish (FIN) AF: 0.241 AC: 2549 AN: 10568

Middle Eastern (MID) AF: 0.313 AC: 92 AN: 294

European-Non Finnish (NFE) AF: 0.272 AC: 18490 AN: 67974

Other (OTH) AF: 0.316 AC: 668 AN: 2112

Alfa AF: 0.292 Hom.: 22133

Bravo AF: 0.321

Asia WGS AF: 0.421 AC: 1459 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.48
DANN	Benign	0.44
PhyloP100		-0.98

Splicing

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

Other links and lift over

dbSNP: rs853803; hg19: chr5-67762103;