rs573179

Variant names:

• chr6-27881898-C-A
• rs573179
• ENST00000812856.1:n.364-5701C>A

Your query was ambiguous. Multiple possible variants found:

• chr6-27881898-C-A
• chr6-27881898-C-T

Variant summary

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

The ENST00000812856.1(ENSG00000305770):​n.364-5701C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.266 in 150,962 control chromosomes in the GnomAD database, including 6,296 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 0.27 (6296 hom., cov: 29)
• Consequence: ENSG00000305770 ENST00000812856.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.00
• Publications: 12 publications found

Genes affected

ENSG00000305770 (HGNC:):

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 = 0.427 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
ENSG00000305770	ENST00000812856.1	n.364-5701C>A		intron_variant	Intron 1 of 1
ENSG00000305770	ENST00000812857.1	n.409-121C>A		intron_variant	Intron 1 of 2
ENSG00000305770	ENST00000812858.1	n.364-5629C>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.265 AC: 40025 AN: 150900 Hom.: 6272 Cov.: 29

Gnomad AFR AF: 0.431

Gnomad AMI AF: 0.358

Gnomad AMR AF: 0.236

Gnomad ASJ AF: 0.144

Gnomad EAS AF: 0.143

Gnomad SAS AF: 0.212

Gnomad FIN AF: 0.155

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.207

Gnomad OTH AF: 0.248

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

GnomAD4 genome AF: 0.266 AC: 40083 AN: 150962 Hom.: 6296 Cov.: 29 AF XY: 0.260 AC XY: 19169 AN XY: 73678

African (AFR) AF: 0.432 AC: 17715 AN: 41016

American (AMR) AF: 0.236 AC: 3574 AN: 15154

Ashkenazi Jewish (ASJ) AF: 0.144 AC: 499 AN: 3464

East Asian (EAS) AF: 0.143 AC: 736 AN: 5136

South Asian (SAS) AF: 0.213 AC: 1018 AN: 4774

European-Finnish (FIN) AF: 0.155 AC: 1596 AN: 10314

Middle Eastern (MID) AF: 0.154 AC: 44 AN: 286

European-Non Finnish (NFE) AF: 0.207 AC: 14063 AN: 67812

Other (OTH) AF: 0.245 AC: 514 AN: 2100

Alfa AF: 0.213 Hom.: 4900

Bravo AF: 0.279

Asia WGS AF: 0.213 AC: 743 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.39
DANN	Benign	0.78
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs573179; hg19: chr6-27849676;