5-86975801-T-C

Position:

• chr5-86975801-T-C

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

ENSG00000249061 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000249061	ENST00000503349.1	n.219+8262T>C		intron_variant		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

Gnomad4 AFR AF: 0.778

Gnomad4 AMR AF: 0.658

Gnomad4 ASJ AF: 0.707

Gnomad4 EAS AF: 0.700

Gnomad4 SAS AF: 0.753

Gnomad4 FIN AF: 0.614

Gnomad4 NFE AF: 0.665

Gnomad4 OTH AF: 0.700

Alfa AF: 0.673 Hom.: 68209

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1073933; hg19: chr5-86271618;