6-31347004-A-G

Variant names:

• chr6-31347004-A-G
• rs2507997
• ENST00000755297.1:n.33-9197A>G

Variant summary

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

The ENST00000755297.1(ENSG00000298396):​n.33-9197A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.203 in 152,196 control chromosomes in the GnomAD database, including 3,424 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 0.20 (3424 hom., cov: 32)
• Consequence: ENSG00000298396 ENST00000755297.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.548
• Publications: 18 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=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.253 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000298396	ENST00000755297.1		n.33-9197A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.203 AC: 30930 AN: 152076 Hom.: 3426 Cov.: 32

Gnomad AFR AF: 0.145

Gnomad AMI AF: 0.298

Gnomad AMR AF: 0.170

Gnomad ASJ AF: 0.206

Gnomad EAS AF: 0.207

Gnomad SAS AF: 0.173

Gnomad FIN AF: 0.148

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.256

Gnomad OTH AF: 0.199

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

GnomAD4 genome AF: 0.203 AC: 30938 AN: 152196 Hom.: 3424 Cov.: 32 AF XY: 0.194 AC XY: 14464 AN XY: 74410

African (AFR) AF: 0.145 AC: 6025 AN: 41532

American (AMR) AF: 0.170 AC: 2601 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.206 AC: 713 AN: 3466

East Asian (EAS) AF: 0.207 AC: 1072 AN: 5182

South Asian (SAS) AF: 0.175 AC: 842 AN: 4820

European-Finnish (FIN) AF: 0.148 AC: 1565 AN: 10598

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.256 AC: 17402 AN: 67988

Other (OTH) AF: 0.198 AC: 419 AN: 2112

Alfa AF: 0.232 Hom.: 7245

Bravo AF: 0.203

Asia WGS AF: 0.193 AC: 670 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	12
DANN	Benign	0.62
PhyloP100		0.55

Splicing

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

Other links and lift over

dbSNP: rs2507997; hg19: chr6-31314781;