6-31314099-G-A

Variant names:

• chr6-31314099-G-A
• rs1634747
• ENST00000755297.1:n.33-42102G>A

Variant summary

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

The ENST00000755297.1(ENSG00000298396):​n.33-42102G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.407 in 144,886 control chromosomes in the GnomAD database, including 16,116 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 0.41 (16116 hom., cov: 28)
• Consequence: ENSG00000298396 ENST00000755297.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.249
• Publications: 6 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 (NFE) allele frequency at 95% confidence interval = 0.413 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.33-42102G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.407 AC: 58949 AN: 144772 Hom.: 16108 Cov.: 28

Gnomad AFR AF: 0.400

Gnomad AMI AF: 0.538

Gnomad AMR AF: 0.343

Gnomad ASJ AF: 0.402

Gnomad EAS AF: 0.283

Gnomad SAS AF: 0.396

Gnomad FIN AF: 0.522

Gnomad MID AF: 0.432

Gnomad NFE AF: 0.417

Gnomad OTH AF: 0.374

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

GnomAD4 genome AF: 0.407 AC: 58993 AN: 144886 Hom.: 16116 Cov.: 28 AF XY: 0.408 AC XY: 28741 AN XY: 70474

African (AFR) AF: 0.400 AC: 15973 AN: 39898

American (AMR) AF: 0.344 AC: 4926 AN: 14340

Ashkenazi Jewish (ASJ) AF: 0.402 AC: 1227 AN: 3056

East Asian (EAS) AF: 0.284 AC: 1362 AN: 4802

South Asian (SAS) AF: 0.396 AC: 1743 AN: 4402

European-Finnish (FIN) AF: 0.522 AC: 5132 AN: 9828

Middle Eastern (MID) AF: 0.438 AC: 114 AN: 260

European-Non Finnish (NFE) AF: 0.417 AC: 27354 AN: 65530

Other (OTH) AF: 0.370 AC: 726 AN: 1960

Alfa AF: 0.407 Hom.: 6364

Asia WGS AF: 0.323 AC: 1089 AN: 3370

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.4
DANN	Benign	0.60
PhyloP100		0.25

Splicing

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

Other links and lift over

dbSNP: rs1634747; hg19: chr6-31281876;