6-32480352-T-C

Variant names:

• chr6-32480352-T-C
• rs4410767
• ENST00000829864.1:n.273+6143T>C

Variant summary

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

The ENST00000829864.1(ENSG00000307923):​n.273+6143T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.36 in 146,556 control chromosomes in the GnomAD database, including 9,397 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 0.36 (9397 hom., cov: 28)
• Consequence: ENSG00000307923 ENST00000829864.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.883
• Publications: 17 publications found

Genes affected

ENSG00000307923 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.399 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000829864.1. 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
	ENSG00000307923	ENST00000829864.1		n.273+6143T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.360 AC: 52694 AN: 146436 Hom.: 9385 Cov.: 28

Gnomad AFR AF: 0.259

Gnomad AMI AF: 0.612

Gnomad AMR AF: 0.408

Gnomad ASJ AF: 0.448

Gnomad EAS AF: 0.348

Gnomad SAS AF: 0.315

Gnomad FIN AF: 0.419

Gnomad MID AF: 0.275

Gnomad NFE AF: 0.398

Gnomad OTH AF: 0.365

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

GnomAD4 genome AF: 0.360 AC: 52737 AN: 146556 Hom.: 9397 Cov.: 28 AF XY: 0.359 AC XY: 25661 AN XY: 71468

African (AFR) AF: 0.259 AC: 10483 AN: 40418

American (AMR) AF: 0.408 AC: 5963 AN: 14614

Ashkenazi Jewish (ASJ) AF: 0.448 AC: 1480 AN: 3306

East Asian (EAS) AF: 0.349 AC: 1748 AN: 5012

South Asian (SAS) AF: 0.316 AC: 1453 AN: 4596

European-Finnish (FIN) AF: 0.419 AC: 4198 AN: 10022

Middle Eastern (MID) AF: 0.270 AC: 76 AN: 282

European-Non Finnish (NFE) AF: 0.399 AC: 26083 AN: 65440

Other (OTH) AF: 0.361 AC: 723 AN: 2000

Alfa AF: 0.371 Hom.: 2842

Asia WGS AF: 0.302 AC: 1052 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	9.0
DANN	Benign	0.81
PhyloP100		0.88

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs4410767;

hg19: chr6-32448129;