rs6850606

Positions:

• chr4-42862679-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.459 in 151,832 control chromosomes in the GnomAD database, including 16,475 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.46 (16475 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.19

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.493 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: 0.459 AC: 69679 AN: 151712 Hom.: 16470 Cov.: 31

Gnomad AFR AF: 0.401

Gnomad AMI AF: 0.353

Gnomad AMR AF: 0.433

Gnomad ASJ AF: 0.583

Gnomad EAS AF: 0.266

Gnomad SAS AF: 0.478

Gnomad FIN AF: 0.527

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.498

Gnomad OTH AF: 0.469

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.459 AC: 69718 AN: 151832 Hom.: 16475 Cov.: 31 AF XY: 0.459 AC XY: 34045 AN XY: 74192

Gnomad4 AFR AF: 0.401

Gnomad4 AMR AF: 0.432

Gnomad4 ASJ AF: 0.583

Gnomad4 EAS AF: 0.266

Gnomad4 SAS AF: 0.480

Gnomad4 FIN AF: 0.527

Gnomad4 NFE AF: 0.498

Gnomad4 OTH AF: 0.464

Alfa AF: 0.488 Hom.: 8780

Bravo AF: 0.447

Asia WGS AF: 0.418 AC: 1458 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.036
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6850606; hg19: chr4-42864696;