6-22757031-C-T

Variant names:

• chr6-22757031-C-T
• rs4607423
• ENST00000420572.2:n.198-11963G>A

Variant summary

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

The ENST00000420572.2(ENSG00000233358):​n.198-11963G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0531 in 151,964 control chromosomes in the GnomAD database, including 294 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 0.053 (294 hom., cov: 31)
• Consequence: ENSG00000233358 ENST00000420572.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.709
• Publications: 0 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=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0717 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.198-11963G>A		intron_variant	Intron 2 of 2	3

Frequencies

GnomAD3 genomes AF: 0.0531 AC: 8060 AN: 151846 Hom.: 293 Cov.: 31

Gnomad AFR AF: 0.0130

Gnomad AMI AF: 0.0440

Gnomad AMR AF: 0.0487

Gnomad ASJ AF: 0.0937

Gnomad EAS AF: 0.00290

Gnomad SAS AF: 0.0214

Gnomad FIN AF: 0.110

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.0733

Gnomad OTH AF: 0.0621

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

GnomAD4 genome AF: 0.0531 AC: 8062 AN: 151964 Hom.: 294 Cov.: 31 AF XY: 0.0545 AC XY: 4044 AN XY: 74248

African (AFR) AF: 0.0130 AC: 538 AN: 41500

American (AMR) AF: 0.0487 AC: 743 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.0937 AC: 325 AN: 3468

East Asian (EAS) AF: 0.00291 AC: 15 AN: 5154

South Asian (SAS) AF: 0.0215 AC: 103 AN: 4798

European-Finnish (FIN) AF: 0.110 AC: 1161 AN: 10544

Middle Eastern (MID) AF: 0.0782 AC: 23 AN: 294

European-Non Finnish (NFE) AF: 0.0734 AC: 4983 AN: 67932

Other (OTH) AF: 0.0619 AC: 131 AN: 2116

Alfa AF: 0.0652 Hom.: 577

Bravo AF: 0.0466

Asia WGS AF: 0.0110 AC: 38 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.32
DANN	Benign	0.71
PhyloP100		-0.71

Splicing

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

Other links and lift over

dbSNP: rs4607423; hg19: chr6-22757260;