rs4840086

Variant names:

• chr6-99760562-A-G
• rs4840086

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 0.337 in 148,956 control chromosomes in the GnomAD database, including 9,920 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 0.34 (9920 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.374

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.422 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.337 AC: 50129 AN: 148854 Hom.: 9924 Cov.: 31

Gnomad AFR AF: 0.115

Gnomad AMI AF: 0.290

Gnomad AMR AF: 0.408

Gnomad ASJ AF: 0.480

Gnomad EAS AF: 0.399

Gnomad SAS AF: 0.372

Gnomad FIN AF: 0.412

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.426

Gnomad OTH AF: 0.381

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

GnomAD4 genome AF: 0.337 AC: 50134 AN: 148956 Hom.: 9920 Cov.: 31 AF XY: 0.337 AC XY: 24474 AN XY: 72642

Gnomad4 AFR AF: 0.115

Gnomad4 AMR AF: 0.408

Gnomad4 ASJ AF: 0.480

Gnomad4 EAS AF: 0.399

Gnomad4 SAS AF: 0.371

Gnomad4 FIN AF: 0.412

Gnomad4 NFE AF: 0.426

Gnomad4 OTH AF: 0.380

Alfa AF: 0.417 Hom.: 15545

Bravo AF: 0.323

Asia WGS AF: 0.326 AC: 1122 AN: 3440

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.2
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4840086; hg19: chr6-100208438;