ENST00000586982.6:n.570-3108A>G

Variant names:

• chr18-35955907-T-C
• rs9951407
• ENST00000586982.6:n.570-3108A>G

Variant summary

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

The ENST00000586982.6(ENSG00000267627):​n.570-3108A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.1 in 152,218 control chromosomes in the GnomAD database, including 882 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 0.10 (882 hom., cov: 32)
• Consequence: ENSG00000267627 ENST00000586982.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.178
• Publications: 4 publications found

Genes affected

ENSG00000267627 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.64).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.125 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105372066	NR_188031.1	n.422-3870A>G		intron_variant	Intron 2 of 2
LOC105372066	NR_188032.1	n.422-3108A>G		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000267627	ENST00000586982.6	n.570-3108A>G		intron_variant	Intron 2 of 3	2
ENSG00000267627	ENST00000589074.1	n.375-3870A>G		intron_variant	Intron 1 of 1	2
ENSG00000267627	ENST00000774003.1	n.143-3870A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.100 AC: 15203 AN: 152100 Hom.: 881 Cov.: 32

Gnomad AFR AF: 0.0615

Gnomad AMI AF: 0.149

Gnomad AMR AF: 0.104

Gnomad ASJ AF: 0.0559

Gnomad EAS AF: 0.0341

Gnomad SAS AF: 0.0697

Gnomad FIN AF: 0.133

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.127

Gnomad OTH AF: 0.0757

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

GnomAD4 genome AF: 0.100 AC: 15217 AN: 152218 Hom.: 882 Cov.: 32 AF XY: 0.0981 AC XY: 7302 AN XY: 74420

African (AFR) AF: 0.0615 AC: 2555 AN: 41562

American (AMR) AF: 0.104 AC: 1583 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.0559 AC: 194 AN: 3472

East Asian (EAS) AF: 0.0340 AC: 176 AN: 5184

South Asian (SAS) AF: 0.0696 AC: 336 AN: 4830

European-Finnish (FIN) AF: 0.133 AC: 1406 AN: 10592

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.127 AC: 8656 AN: 67994

Other (OTH) AF: 0.0764 AC: 161 AN: 2108

Alfa AF: 0.118 Hom.: 2076

Bravo AF: 0.0962

Asia WGS AF: 0.0520 AC: 180 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
CADD	Benign	6.8
DANN	Benign	0.97
PhyloP100		0.18
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs9951407; hg19: chr18-33535870;