13-102845499-G-C

Position:

• chr13-102845499-G-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+5696G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.248 in 152,384 control chromosomes in the GnomAD database, including 5,415 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.25 (5407 hom., cov: 33)
  • Exomes 𝑓: 0.22 (8 hom.)
• Consequence: BIVM-ERCC5 NM_001204425.2 intron
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -0.599

Genes affected

BIVM-ERCC5 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BP6: Variant 13-102845499-G-C is Benign according to our data. Variant chr13-102845499-G-C is described in ClinVar as [Benign]. Clinvar id is 1242141.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.383 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BIVM-ERCC5	NM_001204425.2	c.1450+5696G>C		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.248 AC: 37715 AN: 151944 Hom.: 5401 Cov.: 33

Gnomad AFR AF: 0.382

Gnomad AMI AF: 0.177

Gnomad AMR AF: 0.255

Gnomad ASJ AF: 0.221

Gnomad EAS AF: 0.396

Gnomad SAS AF: 0.195

Gnomad FIN AF: 0.173

Gnomad MID AF: 0.264

Gnomad NFE AF: 0.172

Gnomad OTH AF: 0.235

GnomAD4 exome AF: 0.216 AC: 69 AN: 320 Hom.: 8 Cov.: 0 AF XY: 0.179 AC XY: 33 AN XY: 184

Gnomad4 AFR exome AF: 0.500

Gnomad4 AMR exome AF: 0.167

Gnomad4 ASJ exome AF: 0.100

Gnomad4 EAS exome AF: 0.375

Gnomad4 SAS exome AF: 0.167

Gnomad4 NFE exome AF: 0.161

Gnomad4 OTH exome AF: 0.238

GnomAD4 genome AF: 0.248 AC: 37752 AN: 152064 Hom.: 5407 Cov.: 33 AF XY: 0.248 AC XY: 18405 AN XY: 74334

Gnomad4 AFR AF: 0.381

Gnomad4 AMR AF: 0.255

Gnomad4 ASJ AF: 0.221

Gnomad4 EAS AF: 0.397

Gnomad4 SAS AF: 0.195

Gnomad4 FIN AF: 0.173

Gnomad4 NFE AF: 0.172

Gnomad4 OTH AF: 0.235

Alfa AF: 0.210 Hom.: 494

Bravo AF: 0.267

Asia WGS AF: 0.312 AC: 1085 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	Apr 09, 2019	- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	2.2
DANN	Benign	0.46

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: rs1323697; hg19: chr13-103497849;