6-28322937-T-G

Variant names:

• chr6-28322937-T-G
• rs742107
• ENST00000723788.1:n.163-869T>G

Variant summary

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

The ENST00000723788.1(ENSG00000294464):​n.163-869T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0872 in 152,322 control chromosomes in the GnomAD database, including 815 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 0.087 (815 hom., cov: 32)
• Consequence: ENSG00000294464 ENST00000723788.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0190
• Publications: 8 publications found

Genes affected

ENSG00000294464 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.296 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000723788.1. 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
	ENSG00000294464	ENST00000723788.1		n.163-869T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0872 AC: 13265 AN: 152206 Hom.: 813 Cov.: 32

Gnomad AFR AF: 0.124

Gnomad AMI AF: 0.0636

Gnomad AMR AF: 0.118

Gnomad ASJ AF: 0.0599

Gnomad EAS AF: 0.308

Gnomad SAS AF: 0.124

Gnomad FIN AF: 0.0520

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.0459

Gnomad OTH AF: 0.0799

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

GnomAD4 genome AF: 0.0872 AC: 13282 AN: 152322 Hom.: 815 Cov.: 32 AF XY: 0.0890 AC XY: 6626 AN XY: 74482

African (AFR) AF: 0.124 AC: 5134 AN: 41560

American (AMR) AF: 0.117 AC: 1798 AN: 15310

Ashkenazi Jewish (ASJ) AF: 0.0599 AC: 208 AN: 3472

East Asian (EAS) AF: 0.308 AC: 1595 AN: 5172

South Asian (SAS) AF: 0.126 AC: 611 AN: 4832

European-Finnish (FIN) AF: 0.0520 AC: 552 AN: 10620

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 292

European-Non Finnish (NFE) AF: 0.0459 AC: 3125 AN: 68040

Other (OTH) AF: 0.0791 AC: 167 AN: 2112

Alfa AF: 0.0668 Hom.: 412

Bravo AF: 0.0942

Asia WGS AF: 0.124 AC: 431 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	9.2
DANN	Benign	0.73
PhyloP100		-0.019

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: rs742107;

hg19: chr6-28290714;