6-24113480-A-T

Variant names:

• chr6-24113480-A-T
• rs28921121
• ENST00000810475.1:n.94-6958A>T

Variant summary

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

The ENST00000810475.1(ENSG00000305332):​n.94-6958A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.209 in 152,224 control chromosomes in the GnomAD database, including 3,844 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 0.21 (3844 hom., cov: 32)
• Consequence: ENSG00000305332 ENST00000810475.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.44
• Publications: 0 publications found

Genes affected

ENSG00000305332 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.521 is higher than 0.05.

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.94-6958A>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.209 AC: 31752 AN: 152106 Hom.: 3836 Cov.: 32

Gnomad AFR AF: 0.137

Gnomad AMI AF: 0.0932

Gnomad AMR AF: 0.205

Gnomad ASJ AF: 0.217

Gnomad EAS AF: 0.537

Gnomad SAS AF: 0.335

Gnomad FIN AF: 0.205

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.222

Gnomad OTH AF: 0.192

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

GnomAD4 genome AF: 0.209 AC: 31783 AN: 152224 Hom.: 3844 Cov.: 32 AF XY: 0.213 AC XY: 15880 AN XY: 74424

African (AFR) AF: 0.137 AC: 5672 AN: 41544

American (AMR) AF: 0.205 AC: 3132 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.217 AC: 754 AN: 3468

East Asian (EAS) AF: 0.537 AC: 2781 AN: 5174

South Asian (SAS) AF: 0.335 AC: 1619 AN: 4832

European-Finnish (FIN) AF: 0.205 AC: 2171 AN: 10596

Middle Eastern (MID) AF: 0.153 AC: 45 AN: 294

European-Non Finnish (NFE) AF: 0.222 AC: 15106 AN: 67996

Other (OTH) AF: 0.198 AC: 418 AN: 2116

Alfa AF: 0.117 Hom.: 218

Bravo AF: 0.204

Asia WGS AF: 0.409 AC: 1423 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	9.2
DANN	Benign	0.63
PhyloP100		1.4

Splicing

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

Other links and lift over

dbSNP: rs28921121; hg19: chr6-24113708;