chr6-31350400-G-A

Variant names:

• chr6-31350400-G-A
• rs4394275
• ENST00000755297.1:n.33-5801G>A

Variant summary

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

The ENST00000755297.1(ENSG00000298396):​n.33-5801G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.265 in 152,090 control chromosomes in the GnomAD database, including 5,481 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 0.26 (5481 hom., cov: 32)
• Consequence: ENSG00000298396 ENST00000755297.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.249
• Publications: 29 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.299 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.33-5801G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.265 AC: 40241 AN: 151972 Hom.: 5480 Cov.: 32

Gnomad AFR AF: 0.304

Gnomad AMI AF: 0.229

Gnomad AMR AF: 0.247

Gnomad ASJ AF: 0.227

Gnomad EAS AF: 0.225

Gnomad SAS AF: 0.228

Gnomad FIN AF: 0.369

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.237

Gnomad OTH AF: 0.249

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

GnomAD4 genome AF: 0.265 AC: 40275 AN: 152090 Hom.: 5481 Cov.: 32 AF XY: 0.268 AC XY: 19906 AN XY: 74348

African (AFR) AF: 0.303 AC: 12588 AN: 41478

American (AMR) AF: 0.248 AC: 3786 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.227 AC: 787 AN: 3472

East Asian (EAS) AF: 0.226 AC: 1166 AN: 5170

South Asian (SAS) AF: 0.228 AC: 1098 AN: 4826

European-Finnish (FIN) AF: 0.369 AC: 3897 AN: 10574

Middle Eastern (MID) AF: 0.272 AC: 80 AN: 294

European-Non Finnish (NFE) AF: 0.238 AC: 16145 AN: 67970

Other (OTH) AF: 0.246 AC: 519 AN: 2106

Alfa AF: 0.246 Hom.: 17955

Bravo AF: 0.258

Asia WGS AF: 0.215 AC: 749 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	9.0
DANN	Benign	0.48
PhyloP100		0.25

Splicing

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

Other links and lift over

dbSNP: rs4394275; hg19: chr6-31318177;