rs6857641

Positions:

• chr4-119322356-T-C
• chr4-119322356-T-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 0.566 in 386,000 control chromosomes in the GnomAD database, including 62,260 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.57 (24456 hom., cov: 32)
  • Exomes 𝑓: 0.57 (37804 hom.)
• Consequence: Unknown
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -0.598

ACMG classification

Verdict is Benign. Variant got -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BP6: Variant 4-119322356-T-C is Benign according to our data. Variant chr4-119322356-T-C is described in ClinVar as [Benign]. Clinvar id is 1268685.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.61 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: 0.567 AC: 86053 AN: 151814 Hom.: 24423 Cov.: 32

Gnomad AFR AF: 0.559

Gnomad AMI AF: 0.449

Gnomad AMR AF: 0.605

Gnomad ASJ AF: 0.621

Gnomad EAS AF: 0.629

Gnomad SAS AF: 0.533

Gnomad FIN AF: 0.512

Gnomad MID AF: 0.564

Gnomad NFE AF: 0.568

Gnomad OTH AF: 0.596

GnomAD4 exome AF: 0.566 AC: 132408 AN: 234068 Hom.: 37804 Cov.: 0 AF XY: 0.565 AC XY: 67952 AN XY: 120234

Gnomad4 AFR exome AF: 0.561

Gnomad4 AMR exome AF: 0.630

Gnomad4 ASJ exome AF: 0.635

Gnomad4 EAS exome AF: 0.549

Gnomad4 SAS exome AF: 0.524

Gnomad4 FIN exome AF: 0.512

Gnomad4 NFE exome AF: 0.567

Gnomad4 OTH exome AF: 0.588

GnomAD4 genome AF: 0.567 AC: 86151 AN: 151932 Hom.: 24456 Cov.: 32 AF XY: 0.564 AC XY: 41868 AN XY: 74244

Gnomad4 AFR AF: 0.559

Gnomad4 AMR AF: 0.605

Gnomad4 ASJ AF: 0.621

Gnomad4 EAS AF: 0.628

Gnomad4 SAS AF: 0.533

Gnomad4 FIN AF: 0.512

Gnomad4 NFE AF: 0.568

Gnomad4 OTH AF: 0.599

Alfa AF: 0.564 Hom.: 3126

Bravo AF: 0.579

Asia WGS AF: 0.634 AC: 2206 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	Nov 11, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.4
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: rs6857641; hg19: chr4-120243511; COSMIC: COSV56789133;