chr5-68896913-C-T

Position:

• chr5-68896913-C-T

Variant summary

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

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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.690

Genes affected

(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/exons	MANE	Protein	UniProt
		n.68896913C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000249335	ENST00000503268.2	n.541+63627G>A		intron_variant		3
ENSG00000249335	ENST00000668535.2	n.544+63627G>A		intron_variant
ENSG00000249335	ENST00000690326.2	n.183-68084G>A		intron_variant

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;