14-87807501-G-T

Variant names:

• chr14-87807501-G-T
• rs2401711
• ENST00000554305.5:n.230+8631C>A

Variant summary

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

The ENST00000554305.5(ENSG00000258807):​n.230+8631C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.661 in 151,944 control chromosomes in the GnomAD database, including 34,344 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 0.66 (34344 hom., cov: 31)
• Consequence: ENSG00000258807 ENST00000554305.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.320
• Publications: 0 publications found

Genes affected

ENSG00000258807 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.863 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000554305.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000258807	ENST00000554305.5	TSL:5	n.230+8631C>A		intron	N/A
	ENSG00000258807	ENST00000554519.1	TSL:3	n.120+8631C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.661 AC: 100312 AN: 151826 Hom.: 34286 Cov.: 31

Gnomad AFR AF: 0.807

Gnomad AMI AF: 0.464

Gnomad AMR AF: 0.714

Gnomad ASJ AF: 0.500

Gnomad EAS AF: 0.885

Gnomad SAS AF: 0.744

Gnomad FIN AF: 0.605

Gnomad MID AF: 0.630

Gnomad NFE AF: 0.556

Gnomad OTH AF: 0.657

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

GnomAD4 genome AF: 0.661 AC: 100433 AN: 151944 Hom.: 34344 Cov.: 31 AF XY: 0.667 AC XY: 49570 AN XY: 74272

African (AFR) AF: 0.808 AC: 33486 AN: 41458

American (AMR) AF: 0.715 AC: 10892 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.500 AC: 1731 AN: 3460

East Asian (EAS) AF: 0.885 AC: 4559 AN: 5152

South Asian (SAS) AF: 0.745 AC: 3584 AN: 4812

European-Finnish (FIN) AF: 0.605 AC: 6405 AN: 10588

Middle Eastern (MID) AF: 0.622 AC: 183 AN: 294

European-Non Finnish (NFE) AF: 0.556 AC: 37776 AN: 67914

Other (OTH) AF: 0.660 AC: 1394 AN: 2112

Alfa AF: 0.594 Hom.: 85066

Bravo AF: 0.673

Asia WGS AF: 0.792 AC: 2753 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.3
DANN	Benign	0.40
PhyloP100		-0.32

Splicing

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

Other links and lift over

dbSNP: rs2401711; hg19: chr14-88273845;