5-86975801-T-C

Variant names:

• chr5-86975801-T-C
• rs1073933
• ENST00000503349.1:n.219+8262T>C

Variant summary

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

The ENST00000503349.1(ENSG00000249061):​n.219+8262T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.698 in 151,854 control chromosomes in the GnomAD database, including 37,259 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 (37259 hom., cov: 31)
• Consequence: ENSG00000249061 ENST00000503349.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.790
• Publications: 4 publications found

Genes affected

ENSG00000249061 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.771 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000249061	ENST00000503349.1	n.219+8262T>C		intron_variant	Intron 1 of 2	2

Frequencies

GnomAD3 genomes AF: 0.698 AC: 105838 AN: 151736 Hom.: 37228 Cov.: 31

Gnomad AFR AF: 0.778

Gnomad AMI AF: 0.718

Gnomad AMR AF: 0.658

Gnomad ASJ AF: 0.707

Gnomad EAS AF: 0.700

Gnomad SAS AF: 0.754

Gnomad FIN AF: 0.614

Gnomad MID AF: 0.807

Gnomad NFE AF: 0.665

Gnomad OTH AF: 0.696

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

GnomAD4 genome AF: 0.698 AC: 105923 AN: 151854 Hom.: 37259 Cov.: 31 AF XY: 0.692 AC XY: 51354 AN XY: 74204

African (AFR) AF: 0.778 AC: 32245 AN: 41448

American (AMR) AF: 0.658 AC: 10018 AN: 15224

Ashkenazi Jewish (ASJ) AF: 0.707 AC: 2453 AN: 3470

East Asian (EAS) AF: 0.700 AC: 3604 AN: 5152

South Asian (SAS) AF: 0.753 AC: 3623 AN: 4810

European-Finnish (FIN) AF: 0.614 AC: 6490 AN: 10570

Middle Eastern (MID) AF: 0.803 AC: 236 AN: 294

European-Non Finnish (NFE) AF: 0.665 AC: 45122 AN: 67864

Other (OTH) AF: 0.700 AC: 1479 AN: 2112

Alfa AF: 0.679 Hom.: 107868

Bravo AF: 0.704

Asia WGS AF: 0.744 AC: 2586 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.38
DANN	Benign	0.67
PhyloP100		-0.79

Splicing

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

Other links and lift over

dbSNP: rs1073933; hg19: chr5-86271618;