3-131504119-C-T

Variant names:

• chr3-131504119-C-T
• rs9843898
• ENST00000655300.1:n.117+1415C>T

Variant summary

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

The NR_189110.1(LOC105374114):​n.106+1415C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.739 in 152,144 control chromosomes in the GnomAD database, including 42,791 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 0.74 (42791 hom., cov: 32)
• Consequence: LOC105374114 NR_189110.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.79
• Publications: 3 publications found

Genes affected

ENSG00000248468 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.896 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_189110.1. 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
	LOC105374114	NR_189110.1		n.106+1415C>T		intron	N/A
	LOC105374114	NR_189111.1		n.106+1415C>T		intron	N/A
	LOC105374114	NR_189112.1		n.94+1117C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000248468	ENST00000655300.1		n.117+1415C>T		intron	N/A
	ENSG00000248468	ENST00000655982.1		n.55+1021C>T		intron	N/A
	ENSG00000248468	ENST00000660541.1		n.146+1025C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.739 AC: 112311 AN: 152026 Hom.: 42734 Cov.: 32

Gnomad AFR AF: 0.903

Gnomad AMI AF: 0.726

Gnomad AMR AF: 0.612

Gnomad ASJ AF: 0.783

Gnomad EAS AF: 0.365

Gnomad SAS AF: 0.617

Gnomad FIN AF: 0.667

Gnomad MID AF: 0.813

Gnomad NFE AF: 0.713

Gnomad OTH AF: 0.741

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

GnomAD4 genome AF: 0.739 AC: 112418 AN: 152144 Hom.: 42791 Cov.: 32 AF XY: 0.731 AC XY: 54344 AN XY: 74362

African (AFR) AF: 0.904 AC: 37534 AN: 41536

American (AMR) AF: 0.612 AC: 9347 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.783 AC: 2717 AN: 3472

East Asian (EAS) AF: 0.365 AC: 1889 AN: 5172

South Asian (SAS) AF: 0.617 AC: 2972 AN: 4814

European-Finnish (FIN) AF: 0.667 AC: 7037 AN: 10558

Middle Eastern (MID) AF: 0.806 AC: 237 AN: 294

European-Non Finnish (NFE) AF: 0.713 AC: 48458 AN: 68000

Other (OTH) AF: 0.743 AC: 1566 AN: 2108

Alfa AF: 0.709 Hom.: 6519

Bravo AF: 0.738

Asia WGS AF: 0.545 AC: 1898 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.31
DANN	Benign	0.40
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs9843898; hg19: chr3-131222963;