rs10420252

Positions:

• chr19-35648270-G-A

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 0.0973 in 153,178 control chromosomes in the GnomAD database, including 785 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

• Frequency:
  • Genomes: 𝑓 0.097 (776 hom., cov: 32)
  • Exomes 𝑓: 0.12 (9 hom.)
• Consequence: Unknown
• Clinical Significance: Benign/Likely benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: 1.66

ACMG classification

Verdict is Benign. Variant got -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.64).
• BP6: Variant 19-35648270-G-A is Benign according to our data. Variant chr19-35648270-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 328837.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.134 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0971 AC: 14778 AN: 152138 Hom.: 773 Cov.: 32

Gnomad AFR AF: 0.0934

Gnomad AMI AF: 0.211

Gnomad AMR AF: 0.139

Gnomad ASJ AF: 0.0421

Gnomad EAS AF: 0.136

Gnomad SAS AF: 0.0951

Gnomad FIN AF: 0.113

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0864

Gnomad OTH AF: 0.0918

GnomAD4 exome AF: 0.119 AC: 110 AN: 922 Hom.: 9 Cov.: 0 AF XY: 0.124 AC XY: 71 AN XY: 574

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.177

Gnomad4 SAS exome AF: 0.113

Gnomad4 FIN exome AF: 0.500

Gnomad4 NFE exome AF: 0.111

Gnomad4 OTH exome AF: 0.0455

GnomAD4 genome AF: 0.0972 AC: 14799 AN: 152256 Hom.: 776 Cov.: 32 AF XY: 0.0993 AC XY: 7393 AN XY: 74424

Gnomad4 AFR AF: 0.0936

Gnomad4 AMR AF: 0.139

Gnomad4 ASJ AF: 0.0421

Gnomad4 EAS AF: 0.136

Gnomad4 SAS AF: 0.0952

Gnomad4 FIN AF: 0.113

Gnomad4 NFE AF: 0.0864

Gnomad4 OTH AF: 0.0918

Alfa AF: 0.0862 Hom.: 589

Bravo AF: 0.101

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Mitochondrial complex IV deficiency, nuclear type 1 Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

- -

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 18, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
CADD	Benign	13
DANN	Benign	0.90

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: rs10420252; hg19: chr19-36139172;