rs6518580

Variant names:

• chr22-19748331-T-C
• rs6518580
• ENST00000816392.1:n.*191A>G

Your query was ambiguous. Multiple possible variants found:

• chr22-19748331-T-C
• chr22-19748331-T-G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000816392.1(ENSG00000306238):​n.*191A>G variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. 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: ENSG00000306238 ENST00000816392.1 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.25
• Publications: 5 publications found

Genes affected

ENSG00000306238 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000816392.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000306238	ENST00000816392.1		n.*191A>G		downstream_gene	N/A

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

African (AFR) AF: 0.589 AC: 24309 AN: 41274

American (AMR) AF: 0.586 AC: 8926 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.659 AC: 2279 AN: 3458

East Asian (EAS) AF: 0.584 AC: 2986 AN: 5114

South Asian (SAS) AF: 0.681 AC: 3270 AN: 4804

European-Finnish (FIN) AF: 0.485 AC: 5069 AN: 10452

Middle Eastern (MID) AF: 0.578 AC: 170 AN: 294

European-Non Finnish (NFE) AF: 0.569 AC: 38541 AN: 67740

Other (OTH) AF: 0.574 AC: 1212 AN: 2110

Alfa AF: 0.575 Hom.: 94644

Bravo AF: 0.585

Asia WGS AF: 0.593 AC: 2062 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.082
DANN	Benign	0.54
PhyloP100		-1.3

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs6518580;

hg19: chr22-19735854;