ENST00000416595.1:n.63-388A>C

Variant names:

• chr6-25054937-T-G
• rs458664
• ENST00000416595.1:n.63-388A>C

Variant summary

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

The ENST00000416595.1(ENSG00000223623):​n.63-388A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.575 in 152,028 control chromosomes in the GnomAD database, including 26,817 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 0.57 (26815 hom., cov: 32)
  • Exomes 𝑓: 1.0 (2 hom.)
• Consequence: ENSG00000223623 ENST00000416595.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.423
• Publications: 5 publications found

Genes affected

ENSG00000223623 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.718 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000416595.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000223623	ENST00000416595.1	TSL:3	n.63-388A>C		intron	N/A
	ENSG00000229313	ENST00000428903.1	TSL:5	n.79-26T>G		intron	N/A
	ENSG00000288887	ENST00000761912.1		n.735-23676T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.575 AC: 87328 AN: 151906 Hom.: 26804 Cov.: 32

Gnomad AFR AF: 0.343

Gnomad AMI AF: 0.736

Gnomad AMR AF: 0.590

Gnomad ASJ AF: 0.564

Gnomad EAS AF: 0.738

Gnomad SAS AF: 0.663

Gnomad FIN AF: 0.700

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.674

Gnomad OTH AF: 0.563

GnomAD4 exome AF: 1.00 AC: 4 AN: 4 Hom.: 2 Cov.: 0 AF XY: 1.00 AC XY: 2 AN XY: 2

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 1.00 AC: 2 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 1.00 AC: 2 AN: 2

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.575 AC: 87366 AN: 152024 Hom.: 26815 Cov.: 32 AF XY: 0.578 AC XY: 42922 AN XY: 74310

African (AFR) AF: 0.343 AC: 14196 AN: 41412

American (AMR) AF: 0.590 AC: 9012 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.564 AC: 1958 AN: 3470

East Asian (EAS) AF: 0.737 AC: 3807 AN: 5164

South Asian (SAS) AF: 0.663 AC: 3202 AN: 4828

European-Finnish (FIN) AF: 0.700 AC: 7397 AN: 10562

Middle Eastern (MID) AF: 0.456 AC: 134 AN: 294

European-Non Finnish (NFE) AF: 0.673 AC: 45794 AN: 67996

Other (OTH) AF: 0.568 AC: 1196 AN: 2106

Alfa AF: 0.638 Hom.: 134002

Bravo AF: 0.553

Asia WGS AF: 0.690 AC: 2397 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.1
DANN	Benign	0.70
PhyloP100		-0.42

Splicing

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

Other links and lift over

dbSNP: rs458664; hg19: chr6-25055165;