ENST00000755297.1:n.32+39105A>G

Variant names:

• chr6-31310211-A-G
• rs7755852
• ENST00000755297.1:n.32+39105A>G

Variant summary

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

The ENST00000755297.1(ENSG00000298396):​n.32+39105A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.492 in 146,918 control chromosomes in the GnomAD database, including 21,266 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 0.49 (21266 hom., cov: 29)
• Consequence: ENSG00000298396 ENST00000755297.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.330
• Publications: 13 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=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.568 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000298396	ENST00000755297.1	n.32+39105A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.492 AC: 72294 AN: 146806 Hom.: 21255 Cov.: 29

Gnomad AFR AF: 0.364

Gnomad AMI AF: 0.672

Gnomad AMR AF: 0.426

Gnomad ASJ AF: 0.583

Gnomad EAS AF: 0.578

Gnomad SAS AF: 0.473

Gnomad FIN AF: 0.501

Gnomad MID AF: 0.458

Gnomad NFE AF: 0.572

Gnomad OTH AF: 0.464

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

GnomAD4 genome AF: 0.492 AC: 72322 AN: 146918 Hom.: 21266 Cov.: 29 AF XY: 0.487 AC XY: 34784 AN XY: 71436

African (AFR) AF: 0.364 AC: 14577 AN: 40072

American (AMR) AF: 0.426 AC: 6203 AN: 14562

Ashkenazi Jewish (ASJ) AF: 0.583 AC: 2002 AN: 3432

East Asian (EAS) AF: 0.578 AC: 2450 AN: 4240

South Asian (SAS) AF: 0.473 AC: 2153 AN: 4550

European-Finnish (FIN) AF: 0.501 AC: 5044 AN: 10076

Middle Eastern (MID) AF: 0.458 AC: 131 AN: 286

European-Non Finnish (NFE) AF: 0.572 AC: 38218 AN: 66776

Other (OTH) AF: 0.464 AC: 938 AN: 2022

Alfa AF: 0.529 Hom.: 20160

Asia WGS AF: 0.445 AC: 1441 AN: 3240

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	4.7
DANN	Benign	0.31
PhyloP100		0.33

Splicing

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

Other links and lift over

dbSNP: rs7755852; hg19: chr6-31277988;