rs6840253

Variant names:

• chr4-692774-A-G
• rs6840253

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 0.173 in 152,174 control chromosomes in the GnomAD database, including 2,892 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 0.17 (2892 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.102
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.302 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: 0.173 AC: 26246 AN: 152054 Hom.: 2889 Cov.: 33

Gnomad AFR AF: 0.301

Gnomad AMI AF: 0.0866

Gnomad AMR AF: 0.0959

Gnomad ASJ AF: 0.137

Gnomad EAS AF: 0.315

Gnomad SAS AF: 0.192

Gnomad FIN AF: 0.136

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.109

Gnomad OTH AF: 0.167

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

GnomAD4 genome AF: 0.173 AC: 26272 AN: 152174 Hom.: 2892 Cov.: 33 AF XY: 0.172 AC XY: 12825 AN XY: 74402

African (AFR) AF: 0.300 AC: 12460 AN: 41470

American (AMR) AF: 0.0957 AC: 1463 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.137 AC: 476 AN: 3470

East Asian (EAS) AF: 0.314 AC: 1623 AN: 5164

South Asian (SAS) AF: 0.191 AC: 925 AN: 4834

European-Finnish (FIN) AF: 0.136 AC: 1441 AN: 10608

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.109 AC: 7412 AN: 68018

Other (OTH) AF: 0.173 AC: 365 AN: 2112

Alfa AF: 0.135 Hom.: 3573

Bravo AF: 0.177

Asia WGS AF: 0.240 AC: 834 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.5
DANN	Benign	0.67
PhyloP100		-0.10

Splicing

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

Other links and lift over

dbSNP: rs6840253; hg19: chr4-686563;