rs6813642

Positions:

• chr4-85152307-T-G

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 0.191 in 152,138 control chromosomes in the GnomAD database, including 3,157 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 0.19 (3157 hom., cov: 33)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.299

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.284 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.85152307T>G		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.191 AC: 29060 AN: 152020 Hom.: 3157 Cov.: 33

Gnomad AFR AF: 0.288

Gnomad AMI AF: 0.208

Gnomad AMR AF: 0.179

Gnomad ASJ AF: 0.132

Gnomad EAS AF: 0.0626

Gnomad SAS AF: 0.175

Gnomad FIN AF: 0.146

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.156

Gnomad OTH AF: 0.180

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

GnomAD4 genome AF: 0.191 AC: 29087 AN: 152138 Hom.: 3157 Cov.: 33 AF XY: 0.189 AC XY: 14083 AN XY: 74400

Gnomad4 AFR AF: 0.288

Gnomad4 AMR AF: 0.179

Gnomad4 ASJ AF: 0.132

Gnomad4 EAS AF: 0.0628

Gnomad4 SAS AF: 0.176

Gnomad4 FIN AF: 0.146

Gnomad4 NFE AF: 0.156

Gnomad4 OTH AF: 0.178

Alfa AF: 0.174 Hom.: 431

Bravo AF: 0.195

Asia WGS AF: 0.127 AC: 444 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.1
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6813642; hg19: chr4-86073460;