ENST00000687064.1:n.136+771C>G

Variant names:

• chr14-100684675-C-G
• rs11620937
• ENST00000687064.1:n.136+771C>G

Variant summary

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

The ENST00000687064.1(ENSG00000289278):​n.136+771C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.479 in 151,916 control chromosomes in the GnomAD database, including 21,569 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 0.48 (21569 hom., cov: 31)
• Consequence: ENSG00000289278 ENST00000687064.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.25
• Publications: 4 publications found

Genes affected

ENSG00000289278 (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 = 0.676 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
ENSG00000289278	ENST00000687064.1	n.136+771C>G		intron_variant	Intron 1 of 1
ENSG00000289278	ENST00000701818.1	n.102+771C>G		intron_variant	Intron 1 of 1
ENSG00000258717	ENST00000761489.1	n.255-8127G>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.479 AC: 72774 AN: 151798 Hom.: 21573 Cov.: 31

Gnomad AFR AF: 0.147

Gnomad AMI AF: 0.722

Gnomad AMR AF: 0.462

Gnomad ASJ AF: 0.666

Gnomad EAS AF: 0.242

Gnomad SAS AF: 0.436

Gnomad FIN AF: 0.544

Gnomad MID AF: 0.658

Gnomad NFE AF: 0.682

Gnomad OTH AF: 0.523

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

GnomAD4 genome AF: 0.479 AC: 72774 AN: 151916 Hom.: 21569 Cov.: 31 AF XY: 0.471 AC XY: 34995 AN XY: 74242

African (AFR) AF: 0.147 AC: 6069 AN: 41406

American (AMR) AF: 0.462 AC: 7052 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.666 AC: 2311 AN: 3468

East Asian (EAS) AF: 0.242 AC: 1252 AN: 5180

South Asian (SAS) AF: 0.439 AC: 2112 AN: 4808

European-Finnish (FIN) AF: 0.544 AC: 5722 AN: 10522

Middle Eastern (MID) AF: 0.656 AC: 193 AN: 294

European-Non Finnish (NFE) AF: 0.682 AC: 46314 AN: 67944

Other (OTH) AF: 0.517 AC: 1092 AN: 2112

Alfa AF: 0.446 Hom.: 1539

Bravo AF: 0.459

Asia WGS AF: 0.292 AC: 1017 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.28
DANN	Benign	0.43
PhyloP100		-2.3

Splicing

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

Other links and lift over

dbSNP: rs11620937; hg19: chr14-101151012;