chr6-22752818-A-G

Variant names:

• chr6-22752818-A-G
• rs7356884
• ENST00000420572.2:n.198-7750T>C

Variant summary

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

The ENST00000420572.2(ENSG00000233358):​n.198-7750T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0623 in 151,892 control chromosomes in the GnomAD database, including 399 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 0.062 (399 hom., cov: 32)
• Consequence: ENSG00000233358 ENST00000420572.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.54
• Publications: 5 publications found

Genes affected

ENSG00000233358 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.198 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
ENSG00000233358	ENST00000420572.2	n.198-7750T>C		intron_variant	Intron 2 of 2	3

Frequencies

GnomAD3 genomes AF: 0.0623 AC: 9457 AN: 151776 Hom.: 397 Cov.: 32

Gnomad AFR AF: 0.0692

Gnomad AMI AF: 0.0866

Gnomad AMR AF: 0.0594

Gnomad ASJ AF: 0.0447

Gnomad EAS AF: 0.208

Gnomad SAS AF: 0.137

Gnomad FIN AF: 0.0733

Gnomad MID AF: 0.0318

Gnomad NFE AF: 0.0418

Gnomad OTH AF: 0.0526

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

GnomAD4 genome AF: 0.0623 AC: 9467 AN: 151892 Hom.: 399 Cov.: 32 AF XY: 0.0660 AC XY: 4900 AN XY: 74228

African (AFR) AF: 0.0690 AC: 2864 AN: 41478

American (AMR) AF: 0.0595 AC: 907 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.0447 AC: 155 AN: 3468

East Asian (EAS) AF: 0.208 AC: 1060 AN: 5098

South Asian (SAS) AF: 0.137 AC: 658 AN: 4802

European-Finnish (FIN) AF: 0.0733 AC: 775 AN: 10574

Middle Eastern (MID) AF: 0.0377 AC: 11 AN: 292

European-Non Finnish (NFE) AF: 0.0418 AC: 2841 AN: 67920

Other (OTH) AF: 0.0554 AC: 117 AN: 2112

Alfa AF: 0.0583 Hom.: 234

Bravo AF: 0.0615

Asia WGS AF: 0.184 AC: 638 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.13
DANN	Benign	0.45
PhyloP100		-2.5

Splicing

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

Other links and lift over

dbSNP: rs7356884; hg19: chr6-22753047;