ENST00000690557.2:n.64-33051C>G

Variant names:

• chr6-119516757-C-G
• rs2036256
• ENST00000690557.2:n.64-33051C>G

Variant summary

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

The ENST00000690557.2(ENSG00000287100):​n.64-33051C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.596 in 151,968 control chromosomes in the GnomAD database, including 27,489 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 0.60 (27489 hom., cov: 32)
• Consequence: ENSG00000287100 ENST00000690557.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0400
• Publications: 3 publications found

Genes affected

ENSG00000287100 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.715 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
ENSG00000287100	ENST00000690557.2	n.64-33051C>G		intron_variant	Intron 1 of 3
ENSG00000287100	ENST00000692359.3	n.92-33051C>G		intron_variant	Intron 1 of 3
ENSG00000287100	ENST00000701050.2	n.77-33051C>G		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.596 AC: 90497 AN: 151850 Hom.: 27458 Cov.: 32

Gnomad AFR AF: 0.683

Gnomad AMI AF: 0.508

Gnomad AMR AF: 0.614

Gnomad ASJ AF: 0.540

Gnomad EAS AF: 0.713

Gnomad SAS AF: 0.737

Gnomad FIN AF: 0.539

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.533

Gnomad OTH AF: 0.587

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

GnomAD4 genome AF: 0.596 AC: 90586 AN: 151968 Hom.: 27489 Cov.: 32 AF XY: 0.600 AC XY: 44548 AN XY: 74274

African (AFR) AF: 0.683 AC: 28330 AN: 41478

American (AMR) AF: 0.614 AC: 9374 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.540 AC: 1875 AN: 3470

East Asian (EAS) AF: 0.712 AC: 3678 AN: 5164

South Asian (SAS) AF: 0.736 AC: 3544 AN: 4818

European-Finnish (FIN) AF: 0.539 AC: 5685 AN: 10556

Middle Eastern (MID) AF: 0.636 AC: 187 AN: 294

European-Non Finnish (NFE) AF: 0.533 AC: 36197 AN: 67906

Other (OTH) AF: 0.594 AC: 1254 AN: 2112

Alfa AF: 0.382 Hom.: 896

Bravo AF: 0.601

Asia WGS AF: 0.739 AC: 2571 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.85
DANN	Benign	0.23
PhyloP100		-0.040

Splicing

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

Other links and lift over

dbSNP: rs2036256; hg19: chr6-119837922; COSMIC: COSV69422508;