chr6-31318158-G-T

Variant names:

• chr6-31318158-G-T
• rs3130690
• ENST00000755297.1:n.33-38043G>T

Variant summary

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

The ENST00000755297.1(ENSG00000298396):​n.33-38043G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.127 in 144,480 control chromosomes in the GnomAD database, including 3,000 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 0.13 (3000 hom., cov: 27)
• Consequence: ENSG00000298396 ENST00000755297.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.575
• Publications: 4 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=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.142 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.33-38043G>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.127 AC: 18364 AN: 144372 Hom.: 3001 Cov.: 27

Gnomad AFR AF: 0.122

Gnomad AMI AF: 0.180

Gnomad AMR AF: 0.120

Gnomad ASJ AF: 0.203

Gnomad EAS AF: 0.0795

Gnomad SAS AF: 0.0800

Gnomad FIN AF: 0.0577

Gnomad MID AF: 0.0775

Gnomad NFE AF: 0.145

Gnomad OTH AF: 0.135

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

GnomAD4 genome AF: 0.127 AC: 18364 AN: 144480 Hom.: 3000 Cov.: 27 AF XY: 0.121 AC XY: 8508 AN XY: 70314

African (AFR) AF: 0.122 AC: 4841 AN: 39576

American (AMR) AF: 0.120 AC: 1713 AN: 14284

Ashkenazi Jewish (ASJ) AF: 0.203 AC: 617 AN: 3042

East Asian (EAS) AF: 0.0793 AC: 379 AN: 4782

South Asian (SAS) AF: 0.0792 AC: 348 AN: 4392

European-Finnish (FIN) AF: 0.0577 AC: 571 AN: 9894

Middle Eastern (MID) AF: 0.0682 AC: 18 AN: 264

European-Non Finnish (NFE) AF: 0.145 AC: 9464 AN: 65464

Other (OTH) AF: 0.135 AC: 268 AN: 1978

Alfa AF: 0.113 Hom.: 545

Asia WGS AF: 0.110 AC: 373 AN: 3374

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.5
DANN	Benign	0.46
PhyloP100		-0.57

Splicing

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

Other links and lift over

dbSNP: rs3130690; hg19: chr6-31285935;