rs3134792

Variant names:

• chr6-31344549-T-G
• rs3134792
• ENST00000755297.1:n.33-11652T>G

Variant summary

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

The ENST00000755297.1(ENSG00000298396):​n.33-11652T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0878 in 152,092 control chromosomes in the GnomAD database, including 699 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 0.088 (699 hom., cov: 32)
• Consequence: ENSG00000298396 ENST00000755297.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.399
• Publications: 57 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 = 0.117 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.33-11652T>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0879 AC: 13351 AN: 151974 Hom.: 697 Cov.: 32

Gnomad AFR AF: 0.0553

Gnomad AMI AF: 0.151

Gnomad AMR AF: 0.0425

Gnomad ASJ AF: 0.0473

Gnomad EAS AF: 0.0914

Gnomad SAS AF: 0.111

Gnomad FIN AF: 0.0800

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.119

Gnomad OTH AF: 0.0670

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

GnomAD4 genome AF: 0.0878 AC: 13358 AN: 152092 Hom.: 699 Cov.: 32 AF XY: 0.0849 AC XY: 6312 AN XY: 74356

African (AFR) AF: 0.0553 AC: 2294 AN: 41478

American (AMR) AF: 0.0424 AC: 648 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0473 AC: 164 AN: 3470

East Asian (EAS) AF: 0.0908 AC: 469 AN: 5164

South Asian (SAS) AF: 0.112 AC: 540 AN: 4808

European-Finnish (FIN) AF: 0.0800 AC: 846 AN: 10578

Middle Eastern (MID) AF: 0.0408 AC: 12 AN: 294

European-Non Finnish (NFE) AF: 0.119 AC: 8104 AN: 67986

Other (OTH) AF: 0.0677 AC: 143 AN: 2112

Alfa AF: 0.104 Hom.: 1272

Bravo AF: 0.0820

Asia WGS AF: 0.0960 AC: 332 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	8.3
DANN	Benign	0.59
PhyloP100		0.40

Splicing

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

Other links and lift over

dbSNP: rs3134792; hg19: chr6-31312326;