rs6550783

Variant names:

• chr3-23702595-A-G
• rs6550783

Your query was ambiguous. Multiple possible variants found:

• chr3-23702595-A-G
• chr3-23702595-A-T

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 0.564 in 152,190 control chromosomes in the GnomAD database, including 25,678 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 0.56 (25678 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00500

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.778 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: 0.564 AC: 85706 AN: 152070 Hom.: 25633 Cov.: 32

Gnomad AFR AF: 0.784

Gnomad AMI AF: 0.443

Gnomad AMR AF: 0.505

Gnomad ASJ AF: 0.556

Gnomad EAS AF: 0.311

Gnomad SAS AF: 0.486

Gnomad FIN AF: 0.441

Gnomad MID AF: 0.642

Gnomad NFE AF: 0.487

Gnomad OTH AF: 0.574

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

GnomAD4 genome AF: 0.564 AC: 85807 AN: 152190 Hom.: 25678 Cov.: 32 AF XY: 0.559 AC XY: 41558 AN XY: 74406

Gnomad4 AFR AF: 0.785

Gnomad4 AMR AF: 0.505

Gnomad4 ASJ AF: 0.556

Gnomad4 EAS AF: 0.311

Gnomad4 SAS AF: 0.484

Gnomad4 FIN AF: 0.441

Gnomad4 NFE AF: 0.487

Gnomad4 OTH AF: 0.572

Alfa AF: 0.509 Hom.: 27882

Bravo AF: 0.577

Asia WGS AF: 0.432 AC: 1503 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	5.1
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6550783; hg19: chr3-23744086;