6-58143645-A-G

Variant names:

• chr6-58143645-A-G
• rs1224796
• ENST00000457561.3:n.185-18965A>G

Variant summary

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

The ENST00000457561.3(ENSG00000225096):​n.185-18965A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.508 in 151,504 control chromosomes in the GnomAD database, including 21,701 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 0.51 (21701 hom., cov: 31)
• Consequence: ENSG00000225096 ENST00000457561.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.43
• Publications: 1 publications found

Genes affected

ENSG00000225096 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.758 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
ENSG00000225096	ENST00000457561.3	n.185-18965A>G		intron_variant	Intron 2 of 3	5
ENSG00000225096	ENST00000641631.1	n.151-18965A>G		intron_variant	Intron 2 of 6
ENSG00000225096	ENST00000641775.1	n.317-18965A>G		intron_variant	Intron 3 of 5

Frequencies

GnomAD3 genomes AF: 0.508 AC: 76830 AN: 151386 Hom.: 21667 Cov.: 31

Gnomad AFR AF: 0.765

Gnomad AMI AF: 0.386

Gnomad AMR AF: 0.360

Gnomad ASJ AF: 0.498

Gnomad EAS AF: 0.412

Gnomad SAS AF: 0.404

Gnomad FIN AF: 0.347

Gnomad MID AF: 0.383

Gnomad NFE AF: 0.427

Gnomad OTH AF: 0.483

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

GnomAD4 genome AF: 0.508 AC: 76923 AN: 151504 Hom.: 21701 Cov.: 31 AF XY: 0.499 AC XY: 36977 AN XY: 74044

African (AFR) AF: 0.765 AC: 31643 AN: 41386

American (AMR) AF: 0.361 AC: 5478 AN: 15194

Ashkenazi Jewish (ASJ) AF: 0.498 AC: 1719 AN: 3454

East Asian (EAS) AF: 0.412 AC: 2103 AN: 5106

South Asian (SAS) AF: 0.404 AC: 1941 AN: 4808

European-Finnish (FIN) AF: 0.347 AC: 3662 AN: 10562

Middle Eastern (MID) AF: 0.388 AC: 114 AN: 294

European-Non Finnish (NFE) AF: 0.427 AC: 28886 AN: 67682

Other (OTH) AF: 0.487 AC: 1026 AN: 2108

Alfa AF: 0.453 Hom.: 2038

Bravo AF: 0.524

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.49
DANN	Benign	0.62
PhyloP100		-2.4

Splicing

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

Other links and lift over

dbSNP: rs1224796; hg19: chr6-58469923;