rs3103190

Variant names:

• chr4-42320929-G-A
• rs3103190
• ENST00000503321.1:n.60-37538C>T

Variant summary

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

The ENST00000508911.1(ENSG00000250781):​n.95-21618C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.683 in 152,182 control chromosomes in the GnomAD database, including 35,649 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 0.68 (35649 hom., cov: 34)
• Consequence: ENSG00000250781 ENST00000508911.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.252
• Publications: 3 publications found

Genes affected

ENSG00000250781 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.739 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000508911.1. 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
	LOC105374428	NR_134668.1		n.95-21618C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000250781	ENST00000503321.1	TSL:3	n.60-37538C>T		intron	N/A
	ENSG00000250781	ENST00000508911.1	TSL:2	n.95-21618C>T		intron	N/A
	ENSG00000250781	ENST00000766949.1		n.221-12819C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.683 AC: 103917 AN: 152064 Hom.: 35634 Cov.: 34

Gnomad AFR AF: 0.680

Gnomad AMI AF: 0.520

Gnomad AMR AF: 0.750

Gnomad ASJ AF: 0.764

Gnomad EAS AF: 0.690

Gnomad SAS AF: 0.654

Gnomad FIN AF: 0.733

Gnomad MID AF: 0.718

Gnomad NFE AF: 0.662

Gnomad OTH AF: 0.708

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

GnomAD4 genome AF: 0.683 AC: 103971 AN: 152182 Hom.: 35649 Cov.: 34 AF XY: 0.689 AC XY: 51280 AN XY: 74388

African (AFR) AF: 0.679 AC: 28203 AN: 41524

American (AMR) AF: 0.750 AC: 11472 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.764 AC: 2653 AN: 3472

East Asian (EAS) AF: 0.691 AC: 3576 AN: 5176

South Asian (SAS) AF: 0.654 AC: 3157 AN: 4826

European-Finnish (FIN) AF: 0.733 AC: 7750 AN: 10580

Middle Eastern (MID) AF: 0.704 AC: 207 AN: 294

European-Non Finnish (NFE) AF: 0.662 AC: 44981 AN: 67992

Other (OTH) AF: 0.709 AC: 1498 AN: 2112

Alfa AF: 0.673 Hom.: 116179

Bravo AF: 0.685

Asia WGS AF: 0.676 AC: 2349 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.0
DANN	Benign	0.64
PhyloP100		0.25

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: rs3103190;

hg19: chr4-42322946;