ENST00000755297.1:n.32+2105T>G

Variant names:

• chr6-31273211-T-G
• rs7759127
• ENST00000755297.1:n.32+2105T>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+2105T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.113 in 152,144 control chromosomes in the GnomAD database, including 1,036 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 0.11 (1036 hom., cov: 32)
• Consequence: ENSG00000298396 ENST00000755297.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.846
• Publications: 25 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 = 0.122 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+2105T>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.113 AC: 17243 AN: 152026 Hom.: 1036 Cov.: 32

Gnomad AFR AF: 0.112

Gnomad AMI AF: 0.127

Gnomad AMR AF: 0.119

Gnomad ASJ AF: 0.150

Gnomad EAS AF: 0.105

Gnomad SAS AF: 0.0674

Gnomad FIN AF: 0.0524

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.124

Gnomad OTH AF: 0.121

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

GnomAD4 genome AF: 0.113 AC: 17242 AN: 152144 Hom.: 1036 Cov.: 32 AF XY: 0.108 AC XY: 8037 AN XY: 74368

African (AFR) AF: 0.112 AC: 4639 AN: 41468

American (AMR) AF: 0.118 AC: 1810 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.150 AC: 522 AN: 3472

East Asian (EAS) AF: 0.105 AC: 547 AN: 5192

South Asian (SAS) AF: 0.0671 AC: 323 AN: 4816

European-Finnish (FIN) AF: 0.0524 AC: 555 AN: 10594

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

European-Non Finnish (NFE) AF: 0.124 AC: 8464 AN: 68012

Other (OTH) AF: 0.120 AC: 254 AN: 2108

Alfa AF: 0.117 Hom.: 2080

Bravo AF: 0.120

Asia WGS AF: 0.0870 AC: 305 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	7.9
DANN	Benign	0.51
PhyloP100		-0.85

Splicing

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

Other links and lift over

dbSNP: rs7759127; hg19: chr6-31240988;