6-31433597-C-T

Variant names:

• chr6-31433597-C-T
• rs4346874
• ENST00000673857.1:n.63-29526C>T

Variant summary

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

The ENST00000673857.1(ENSG00000288587):​n.63-29526C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.217 in 151,578 control chromosomes in the GnomAD database, including 4,256 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 0.22 (4256 hom., cov: 31)
• Consequence: ENSG00000288587 ENST00000673857.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.145
• Publications: 12 publications found

Genes affected

ENSG00000288587 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.31 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000673857.1. 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
	ENSG00000288587	ENST00000673857.1		n.63-29526C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.216 AC: 32784 AN: 151458 Hom.: 4248 Cov.: 31

Gnomad AFR AF: 0.314

Gnomad AMI AF: 0.352

Gnomad AMR AF: 0.268

Gnomad ASJ AF: 0.275

Gnomad EAS AF: 0.174

Gnomad SAS AF: 0.228

Gnomad FIN AF: 0.234

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.141

Gnomad OTH AF: 0.206

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

GnomAD4 genome AF: 0.217 AC: 32830 AN: 151578 Hom.: 4256 Cov.: 31 AF XY: 0.222 AC XY: 16414 AN XY: 74066

African (AFR) AF: 0.314 AC: 12940 AN: 41200

American (AMR) AF: 0.268 AC: 4071 AN: 15174

Ashkenazi Jewish (ASJ) AF: 0.275 AC: 954 AN: 3468

East Asian (EAS) AF: 0.174 AC: 895 AN: 5140

South Asian (SAS) AF: 0.227 AC: 1090 AN: 4794

European-Finnish (FIN) AF: 0.234 AC: 2467 AN: 10542

Middle Eastern (MID) AF: 0.228 AC: 67 AN: 294

European-Non Finnish (NFE) AF: 0.141 AC: 9597 AN: 67952

Other (OTH) AF: 0.204 AC: 428 AN: 2102

Alfa AF: 0.167 Hom.: 2157

Bravo AF: 0.222

Asia WGS AF: 0.199 AC: 690 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	6.0
DANN	Benign	0.37
PhyloP100		0.14

Splicing

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

Other links and lift over

dbSNP: rs4346874; hg19: chr6-31401374;