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:58096):

LOC105379013 (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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000507733.3. 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
	ENSG00000248884	ENST00000507733.3	TSL:2	n.347-31799T>C		intron	N/A
	ENSG00000248884	ENST00000701911.2		n.205-31799T>C		intron	N/A
	ENSG00000248884	ENST00000717704.1		n.144-9128T>C		intron	N/A

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 v4.9

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

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

Other links and lift over

dbSNP: rs853803;

hg19: chr5-67762103;