rs727675

Variant names:

• chr14-31264436-G-A
• rs727675
• ENST00000551799.1:n.204+1634G>A

Your query was ambiguous. Multiple possible variants found:

• chr14-31264436-G-A
• chr14-31264436-G-C
• chr14-31264436-G-T

Variant summary

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

The ENST00000551799.1(ENSG00000257831):​n.204+1634G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.538 in 152,072 control chromosomes in the GnomAD database, including 22,664 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 0.54 (22664 hom., cov: 33)
• Consequence: ENSG00000257831 ENST00000551799.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.662
• Publications: 6 publications found

Genes affected

ENSG00000257831 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.721 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000551799.1. 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
	ENSG00000257831	ENST00000551799.1	TSL:3	n.204+1634G>A		intron	N/A
	ENSG00000296926	ENST00000743665.1		n.-230C>T		upstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.538 AC: 81733 AN: 151954 Hom.: 22659 Cov.: 33

Gnomad AFR AF: 0.409

Gnomad AMI AF: 0.492

Gnomad AMR AF: 0.545

Gnomad ASJ AF: 0.533

Gnomad EAS AF: 0.742

Gnomad SAS AF: 0.655

Gnomad FIN AF: 0.653

Gnomad MID AF: 0.510

Gnomad NFE AF: 0.574

Gnomad OTH AF: 0.543

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

GnomAD4 genome AF: 0.538 AC: 81776 AN: 152072 Hom.: 22664 Cov.: 33 AF XY: 0.544 AC XY: 40457 AN XY: 74342

African (AFR) AF: 0.409 AC: 16950 AN: 41470

American (AMR) AF: 0.545 AC: 8331 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.533 AC: 1847 AN: 3468

East Asian (EAS) AF: 0.741 AC: 3833 AN: 5174

South Asian (SAS) AF: 0.656 AC: 3164 AN: 4820

European-Finnish (FIN) AF: 0.653 AC: 6908 AN: 10580

Middle Eastern (MID) AF: 0.507 AC: 148 AN: 292

European-Non Finnish (NFE) AF: 0.574 AC: 39003 AN: 67966

Other (OTH) AF: 0.544 AC: 1145 AN: 2104

Alfa AF: 0.560 Hom.: 63227

Bravo AF: 0.524

Asia WGS AF: 0.699 AC: 2430 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	6.3
DANN	Benign	0.80
PhyloP100		0.66

Splicing

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

Other links and lift over

dbSNP: rs727675; hg19: chr14-31733642;