rs794085

Positions:

• chr19-7629716-C-G

Variant summary

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

The variant allele was found at a frequency of 0.222 in 1,464,596 control chromosomes in the GnomAD database, including 37,448 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.19 (3015 hom., cov: 32)
  • Exomes 𝑓: 0.22 (34433 hom.)
• Consequence: Unknown
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -1.54

ACMG classification

Verdict is Benign. Variant got -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BP6: Variant 19-7629716-C-G is Benign according to our data. Variant chr19-7629716-C-G is described in ClinVar as [Benign]. Clinvar id is 1270843.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.225 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.194 AC: 29476 AN: 152098 Hom.: 3013 Cov.: 32

Gnomad AFR AF: 0.149

Gnomad AMI AF: 0.482

Gnomad AMR AF: 0.174

Gnomad ASJ AF: 0.198

Gnomad EAS AF: 0.121

Gnomad SAS AF: 0.156

Gnomad FIN AF: 0.205

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.228

Gnomad OTH AF: 0.192

GnomAD4 exome AF: 0.225 AC: 295270 AN: 1312380 Hom.: 34433 Cov.: 20 AF XY: 0.224 AC XY: 145292 AN XY: 649488

Gnomad4 AFR exome AF: 0.146

Gnomad4 AMR exome AF: 0.159

Gnomad4 ASJ exome AF: 0.208

Gnomad4 EAS exome AF: 0.130

Gnomad4 SAS exome AF: 0.160

Gnomad4 FIN exome AF: 0.218

Gnomad4 NFE exome AF: 0.239

Gnomad4 OTH exome AF: 0.217

GnomAD4 genome AF: 0.194 AC: 29493 AN: 152216 Hom.: 3015 Cov.: 32 AF XY: 0.191 AC XY: 14239 AN XY: 74408

Gnomad4 AFR AF: 0.149

Gnomad4 AMR AF: 0.174

Gnomad4 ASJ AF: 0.198

Gnomad4 EAS AF: 0.121

Gnomad4 SAS AF: 0.157

Gnomad4 FIN AF: 0.205

Gnomad4 NFE AF: 0.228

Gnomad4 OTH AF: 0.192

Alfa AF: 0.118 Hom.: 188

Bravo AF: 0.193

Asia WGS AF: 0.148 AC: 516 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	Jun 23, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	0.47
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs794085; hg19: chr19-7694602; COSMIC: COSV60696697;