5-68896913-C-T

Variant names:

• chr5-68896913-C-T
• rs4976053
• ENST00000503268.2:n.541+63627G>A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000503268.2(ENSG00000249335):​n.541+63627G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.701 in 152,104 control chromosomes in the GnomAD database, including 37,623 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 (37623 hom., cov: 33)
• Consequence: ENSG00000249335 ENST00000503268.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.690

Genes affected

ENSG00000249335 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.742 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
ENSG00000249335	ENST00000503268.2	n.541+63627G>A		intron_variant	Intron 3 of 3	3
ENSG00000249335	ENST00000668535.2	n.544+63627G>A		intron_variant	Intron 3 of 5
ENSG00000249335	ENST00000690326.2	n.183-68084G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.701 AC: 106610 AN: 151986 Hom.: 37595 Cov.: 33

Gnomad AFR AF: 0.749

Gnomad AMI AF: 0.512

Gnomad AMR AF: 0.753

Gnomad ASJ AF: 0.729

Gnomad EAS AF: 0.664

Gnomad SAS AF: 0.622

Gnomad FIN AF: 0.705

Gnomad MID AF: 0.585

Gnomad NFE AF: 0.671

Gnomad OTH AF: 0.691

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

GnomAD4 genome AF: 0.701 AC: 106698 AN: 152104 Hom.: 37623 Cov.: 33 AF XY: 0.704 AC XY: 52343 AN XY: 74356

Gnomad4 AFR AF: 0.749

Gnomad4 AMR AF: 0.753

Gnomad4 ASJ AF: 0.729

Gnomad4 EAS AF: 0.666

Gnomad4 SAS AF: 0.622

Gnomad4 FIN AF: 0.705

Gnomad4 NFE AF: 0.671

Gnomad4 OTH AF: 0.688

Alfa AF: 0.698 Hom.: 6760

Bravo AF: 0.708

Asia WGS AF: 0.628 AC: 2185 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.55
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4976053; hg19: chr5-68192740;