rs146696563

Variant names:

• chr6-24062560-T-C
• rs146696563
• ENST00000810475.1:n.93+28949T>C

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BP4_Strong BS2

The ENST00000810475.1(ENSG00000305332):​n.93+28949T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00884 in 152,236 control chromosomes in the GnomAD database, including 10 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 0.0088 (10 hom., cov: 31)
• Consequence: ENSG00000305332 ENST00000810475.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.312
• Publications: 1 publications found

Genes affected

ENSG00000305332 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BS2: High Homozygotes in GnomAd4 at 10 gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000810475.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000305332	ENST00000810475.1		n.93+28949T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.00884 AC: 1345 AN: 152118 Hom.: 10 Cov.: 31

Gnomad AFR AF: 0.00176

Gnomad AMI AF: 0.0209

Gnomad AMR AF: 0.00511

Gnomad ASJ AF: 0.00778

Gnomad EAS AF: 0.000965

Gnomad SAS AF: 0.00228

Gnomad FIN AF: 0.0199

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.0132

Gnomad OTH AF: 0.0100

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

GnomAD4 genome AF: 0.00884 AC: 1346 AN: 152236 Hom.: 10 Cov.: 31 AF XY: 0.00846 AC XY: 630 AN XY: 74440

African (AFR) AF: 0.00176 AC: 73 AN: 41550

American (AMR) AF: 0.00510 AC: 78 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.00778 AC: 27 AN: 3470

East Asian (EAS) AF: 0.000967 AC: 5 AN: 5170

South Asian (SAS) AF: 0.00228 AC: 11 AN: 4824

European-Finnish (FIN) AF: 0.0199 AC: 211 AN: 10616

Middle Eastern (MID) AF: 0.0170 AC: 5 AN: 294

European-Non Finnish (NFE) AF: 0.0132 AC: 895 AN: 68008

Other (OTH) AF: 0.0104 AC: 22 AN: 2114

Alfa AF: 0.0120 Hom.: 0

Bravo AF: 0.00747

Asia WGS AF: 0.00231 AC: 8 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.3
DANN	Benign	0.45
PhyloP100		-0.31

Splicing

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

Other links and lift over

dbSNP: rs146696563; hg19: chr6-24062788;