5-63962738-C-G

Position:

• chr5-63962738-C-G

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The variant allele was found at a frequency of 0.491 in 151,978 control chromosomes in the GnomAD database, including 18,681 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

• Frequency: Genomes: 𝑓 0.49 (18681 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.716

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BP6: Variant 5-63962738-C-G is Benign according to our data. Variant chr5-63962738-C-G is described in ClinVar as [Likely_benign]. Clinvar id is 375667.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.737 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.63962738C>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000248285	ENST00000502882.1	n.97-4723G>C		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.491 AC: 74590 AN: 151860 Hom.: 18657 Cov.: 32

Gnomad AFR AF: 0.440

Gnomad AMI AF: 0.699

Gnomad AMR AF: 0.488

Gnomad ASJ AF: 0.531

Gnomad EAS AF: 0.757

Gnomad SAS AF: 0.587

Gnomad FIN AF: 0.426

Gnomad MID AF: 0.642

Gnomad NFE AF: 0.500

Gnomad OTH AF: 0.505

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

GnomAD4 genome AF: 0.491 AC: 74651 AN: 151978 Hom.: 18681 Cov.: 32 AF XY: 0.491 AC XY: 36500 AN XY: 74302

Gnomad4 AFR AF: 0.440

Gnomad4 AMR AF: 0.488

Gnomad4 ASJ AF: 0.531

Gnomad4 EAS AF: 0.757

Gnomad4 SAS AF: 0.585

Gnomad4 FIN AF: 0.426

Gnomad4 NFE AF: 0.500

Gnomad4 OTH AF: 0.506

Alfa AF: 0.479 Hom.: 2152

Bravo AF: 0.491

Asia WGS AF: 0.634 AC: 2206 AN: 3478

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Benign:1

Likely benign, criteria provided, single submitter

clinical testing

GeneDx

Mar 09, 2018

This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	2.4
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6295; hg19: chr5-63258565;