6-31351578-G-T

Variant names:

• chr6-31351578-G-T
• rs2442728
• ENST00000755297.1:n.33-4623G>T

Variant summary

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

The ENST00000755297.1(ENSG00000298396):​n.33-4623G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.371 in 150,192 control chromosomes in the GnomAD database, including 10,658 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 0.37 (10658 hom., cov: 26)
• Consequence: ENSG00000298396 ENST00000755297.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.49
• Publications: 9 publications found

Genes affected

ENSG00000298396 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.422 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000755297.1. 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
	ENSG00000298396	ENST00000755297.1		n.33-4623G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.371 AC: 55700 AN: 150074 Hom.: 10648 Cov.: 26

Gnomad AFR AF: 0.314

Gnomad AMI AF: 0.279

Gnomad AMR AF: 0.410

Gnomad ASJ AF: 0.277

Gnomad EAS AF: 0.323

Gnomad SAS AF: 0.437

Gnomad FIN AF: 0.385

Gnomad MID AF: 0.367

Gnomad NFE AF: 0.400

Gnomad OTH AF: 0.375

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

GnomAD4 genome AF: 0.371 AC: 55749 AN: 150192 Hom.: 10658 Cov.: 26 AF XY: 0.373 AC XY: 27308 AN XY: 73154

African (AFR) AF: 0.314 AC: 12800 AN: 40718

American (AMR) AF: 0.410 AC: 6155 AN: 15022

Ashkenazi Jewish (ASJ) AF: 0.277 AC: 957 AN: 3456

East Asian (EAS) AF: 0.324 AC: 1634 AN: 5044

South Asian (SAS) AF: 0.438 AC: 2064 AN: 4714

European-Finnish (FIN) AF: 0.385 AC: 3951 AN: 10250

Middle Eastern (MID) AF: 0.374 AC: 110 AN: 294

European-Non Finnish (NFE) AF: 0.400 AC: 27047 AN: 67700

Other (OTH) AF: 0.373 AC: 777 AN: 2084

Alfa AF: 0.390 Hom.: 12548

Bravo AF: 0.373

Asia WGS AF: 0.409 AC: 1421 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.81
DANN	Benign	0.33
PhyloP100		-2.5

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: rs2442728;

hg19: chr6-31319355;