13-102845567-T-C

Position:

• chr13-102845567-T-C

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_001204425.2(BIVM-ERCC5):​c.1450+5764T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0933 in 155,428 control chromosomes in the GnomAD database, including 784 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.094 (775 hom., cov: 33)
  • Exomes 𝑓: 0.075 (9 hom.)
• Consequence: BIVM-ERCC5 NM_001204425.2 intron
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -2.59

Genes affected

BIVM-ERCC5 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BP6: Variant 13-102845567-T-C is Benign according to our data. Variant chr13-102845567-T-C is described in ClinVar as [Benign]. Clinvar id is 1238248.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.12 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BIVM-ERCC5	NM_001204425.2	c.1450+5764T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0938 AC: 14264 AN: 152130 Hom.: 774 Cov.: 33

Gnomad AFR AF: 0.0573

Gnomad AMI AF: 0.101

Gnomad AMR AF: 0.0716

Gnomad ASJ AF: 0.106

Gnomad EAS AF: 0.00173

Gnomad SAS AF: 0.0665

Gnomad FIN AF: 0.141

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.122

Gnomad OTH AF: 0.0900

GnomAD4 exome AF: 0.0755 AC: 240 AN: 3180 Hom.: 9 Cov.: 0 AF XY: 0.0795 AC XY: 123 AN XY: 1548

Gnomad4 AFR exome AF: 0.0408

Gnomad4 AMR exome AF: 0.0625

Gnomad4 ASJ exome AF: 0.0776

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.0606

Gnomad4 FIN exome AF: 0.167

Gnomad4 NFE exome AF: 0.104

Gnomad4 OTH exome AF: 0.109

GnomAD4 genome AF: 0.0937 AC: 14265 AN: 152248 Hom.: 775 Cov.: 33 AF XY: 0.0934 AC XY: 6951 AN XY: 74450

Gnomad4 AFR AF: 0.0575

Gnomad4 AMR AF: 0.0715

Gnomad4 ASJ AF: 0.106

Gnomad4 EAS AF: 0.00174

Gnomad4 SAS AF: 0.0655

Gnomad4 FIN AF: 0.141

Gnomad4 NFE AF: 0.122

Gnomad4 OTH AF: 0.0881

Alfa AF: 0.0366 Hom.: 31

Bravo AF: 0.0878

Asia WGS AF: 0.0360 AC: 125 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Jan 10, 2019	- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.7
DANN	Benign	0.33

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs4150247; hg19: chr13-103497917;