6-22752818-A-G

Position:

• chr6-22752818-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000420572.2(ENSG00000233358):​n.198-7750T>C variant causes a intron, non coding transcript 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: ENST00000420572.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.54

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000420572.2	n.198-7750T>C		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR AF: 0.0690

Gnomad4 AMR AF: 0.0595

Gnomad4 ASJ AF: 0.0447

Gnomad4 EAS AF: 0.208

Gnomad4 SAS AF: 0.137

Gnomad4 FIN AF: 0.0733

Gnomad4 NFE AF: 0.0418

Gnomad4 OTH AF: 0.0554

Alfa AF: 0.0499 Hom.: 65

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7356884; hg19: chr6-22753047;