rs6518580

chr22-19748331-T-Cchr22-19748331-T-G

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 0.576 in 151,392 control chromosomes in the GnomAD database, including 25,102 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 0.58 (25102 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.25

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.661 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.576 AC: 87084 AN: 151272 Hom.: 25073 Cov.: 31

Gnomad AFR AF: 0.589

Gnomad AMI AF: 0.447

Gnomad AMR AF: 0.586

Gnomad ASJ AF: 0.659

Gnomad EAS AF: 0.584

Gnomad SAS AF: 0.681

Gnomad FIN AF: 0.485

Gnomad MID AF: 0.582

Gnomad NFE AF: 0.569

Gnomad OTH AF: 0.574

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

GnomAD4 genome AF: 0.576 AC: 87167 AN: 151392 Hom.: 25102 Cov.: 31 AF XY: 0.573 AC XY: 42401 AN XY: 73936

Gnomad4 AFR AF: 0.589

Gnomad4 AMR AF: 0.586

Gnomad4 ASJ AF: 0.659

Gnomad4 EAS AF: 0.584

Gnomad4 SAS AF: 0.681

Gnomad4 FIN AF: 0.485

Gnomad4 NFE AF: 0.569

Gnomad4 OTH AF: 0.574

Alfa AF: 0.580 Hom.: 38054

Bravo AF: 0.585

Asia WGS AF: 0.593 AC: 2062 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	0.082
Dann	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6518580; hg19: chr22-19735854;