rs1399903

Variant names:

• chr3-161676316-T-C
• rs1399903
• ENST00000665274.1:n.116-58126T>C

Variant summary

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

The ENST00000665274.1(ENSG00000288087):​n.116-58126T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0686 in 152,250 control chromosomes in the GnomAD database, including 516 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 0.069 (516 hom., cov: 32)
• Consequence: ENSG00000288087 ENST00000665274.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.165
• Publications: 4 publications found

Genes affected

ENSG00000288087 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.16 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000665274.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000288087	ENST00000665274.1		n.116-58126T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0685 AC: 10423 AN: 152132 Hom.: 513 Cov.: 32

Gnomad AFR AF: 0.0170

Gnomad AMI AF: 0.0186

Gnomad AMR AF: 0.117

Gnomad ASJ AF: 0.112

Gnomad EAS AF: 0.169

Gnomad SAS AF: 0.154

Gnomad FIN AF: 0.0519

Gnomad MID AF: 0.169

Gnomad NFE AF: 0.0755

Gnomad OTH AF: 0.0817

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

GnomAD4 genome AF: 0.0686 AC: 10438 AN: 152250 Hom.: 516 Cov.: 32 AF XY: 0.0709 AC XY: 5277 AN XY: 74442

African (AFR) AF: 0.0170 AC: 706 AN: 41550

American (AMR) AF: 0.118 AC: 1800 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.112 AC: 387 AN: 3470

East Asian (EAS) AF: 0.170 AC: 878 AN: 5174

South Asian (SAS) AF: 0.154 AC: 743 AN: 4818

European-Finnish (FIN) AF: 0.0519 AC: 551 AN: 10614

Middle Eastern (MID) AF: 0.161 AC: 47 AN: 292

European-Non Finnish (NFE) AF: 0.0755 AC: 5135 AN: 68010

Other (OTH) AF: 0.0823 AC: 174 AN: 2114

Alfa AF: 0.0743 Hom.: 90

Bravo AF: 0.0725

Asia WGS AF: 0.163 AC: 567 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.6
DANN	Benign	0.63
PhyloP100		0.17

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1399903;

hg19: chr3-161394104;