rs6813642

Variant names:

• chr4-85152307-T-G
• rs6813642

Variant summary

Our verdict is Benign. The variant received -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: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.299
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.288 AC: 11943 AN: 41480

American (AMR) AF: 0.179 AC: 2739 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.132 AC: 459 AN: 3466

East Asian (EAS) AF: 0.0628 AC: 325 AN: 5176

South Asian (SAS) AF: 0.176 AC: 845 AN: 4806

European-Finnish (FIN) AF: 0.146 AC: 1554 AN: 10610

Middle Eastern (MID) AF: 0.218 AC: 64 AN: 294

European-Non Finnish (NFE) AF: 0.156 AC: 10593 AN: 67994

Other (OTH) AF: 0.178 AC: 376 AN: 2108

Alfa AF: 0.169 Hom.: 813

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
PhyloP100		-0.30

Splicing

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

Other links and lift over

dbSNP: rs6813642; hg19: chr4-86073460;