rs243757

Variant names:

• chr6-54521183-G-A
• rs243757

Your query was ambiguous. Multiple possible variants found:

• chr6-54521183-G-A
• chr6-54521183-G-C

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 0.1 in 152,130 control chromosomes in the GnomAD database, including 1,269 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 (1269 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.23

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.228 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: 0.0999 AC: 15192 AN: 152012 Hom.: 1269 Cov.: 32

Gnomad AFR AF: 0.233

Gnomad AMI AF: 0.0307

Gnomad AMR AF: 0.0604

Gnomad ASJ AF: 0.0510

Gnomad EAS AF: 0.0143

Gnomad SAS AF: 0.0147

Gnomad FIN AF: 0.0256

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.0562

Gnomad OTH AF: 0.0852

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

GnomAD4 genome AF: 0.100 AC: 15208 AN: 152130 Hom.: 1269 Cov.: 32 AF XY: 0.0950 AC XY: 7064 AN XY: 74380

Gnomad4 AFR AF: 0.232

Gnomad4 AMR AF: 0.0602

Gnomad4 ASJ AF: 0.0510

Gnomad4 EAS AF: 0.0143

Gnomad4 SAS AF: 0.0143

Gnomad4 FIN AF: 0.0256

Gnomad4 NFE AF: 0.0562

Gnomad4 OTH AF: 0.0858

Alfa AF: 0.0832 Hom.: 109

Bravo AF: 0.110

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.28
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs243757; hg19: chr6-54385981;