rs243802

Variant names:

• chr6-54443919-G-A
• rs243802

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 0.102 in 152,120 control chromosomes in the GnomAD database, including 1,275 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 0.10 (1275 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.72
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.225 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: 0.102 AC: 15508 AN: 152002 Hom.: 1276 Cov.: 32

Gnomad AFR AF: 0.229

Gnomad AMI AF: 0.0307

Gnomad AMR AF: 0.0618

Gnomad ASJ AF: 0.0397

Gnomad EAS AF: 0.0149

Gnomad SAS AF: 0.0183

Gnomad FIN AF: 0.0305

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.0622

Gnomad OTH AF: 0.0875

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

GnomAD4 genome AF: 0.102 AC: 15520 AN: 152120 Hom.: 1275 Cov.: 32 AF XY: 0.0971 AC XY: 7222 AN XY: 74368

African (AFR) AF: 0.229 AC: 9475 AN: 41458

American (AMR) AF: 0.0617 AC: 943 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0397 AC: 138 AN: 3472

East Asian (EAS) AF: 0.0149 AC: 77 AN: 5166

South Asian (SAS) AF: 0.0181 AC: 87 AN: 4816

European-Finnish (FIN) AF: 0.0305 AC: 324 AN: 10606

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.0622 AC: 4231 AN: 67996

Other (OTH) AF: 0.0880 AC: 186 AN: 2114

Alfa AF: 0.0860 Hom.: 108

Bravo AF: 0.111

Asia WGS AF: 0.0370 AC: 129 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.4
DANN	Benign	0.45
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs243802; hg19: chr6-54308717;