rs6004527

Variant names:

• chr22-25273614-G-A
• rs6004527
• ENST00000823016.1:n.116-3132C>T

Variant summary

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

The ENST00000823016.1(ENSG00000233577):​n.116-3132C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.184 in 151,682 control chromosomes in the GnomAD database, including 3,228 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 0.18 (3228 hom., cov: 32)
• Consequence: ENSG00000233577 ENST00000823016.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0610
• Publications: 4 publications found

Genes affected

ENSG00000233577 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.32 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000823016.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000233577	ENST00000823016.1		n.116-3132C>T		intron	N/A
	ENSG00000233577	ENST00000823017.1		n.403-3132C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.184 AC: 27836 AN: 151564 Hom.: 3218 Cov.: 32

Gnomad AFR AF: 0.324

Gnomad AMI AF: 0.163

Gnomad AMR AF: 0.126

Gnomad ASJ AF: 0.241

Gnomad EAS AF: 0.0460

Gnomad SAS AF: 0.138

Gnomad FIN AF: 0.0845

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.138

Gnomad OTH AF: 0.183

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

GnomAD4 genome AF: 0.184 AC: 27867 AN: 151682 Hom.: 3228 Cov.: 32 AF XY: 0.178 AC XY: 13237 AN XY: 74176

African (AFR) AF: 0.324 AC: 13383 AN: 41278

American (AMR) AF: 0.126 AC: 1916 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.241 AC: 836 AN: 3464

East Asian (EAS) AF: 0.0459 AC: 237 AN: 5160

South Asian (SAS) AF: 0.138 AC: 662 AN: 4800

European-Finnish (FIN) AF: 0.0845 AC: 891 AN: 10550

Middle Eastern (MID) AF: 0.194 AC: 57 AN: 294

European-Non Finnish (NFE) AF: 0.138 AC: 9357 AN: 67870

Other (OTH) AF: 0.180 AC: 379 AN: 2104

Alfa AF: 0.156 Hom.: 910

Bravo AF: 0.194

Asia WGS AF: 0.109 AC: 378 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.8
DANN	Benign	0.46
PhyloP100		-0.061

Splicing

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

Other links and lift over

dbSNP: rs6004527; hg19: chr22-25669581;