rs4669060

Variant names:

• chr2-6338296-C-A
• rs4669060
• ENST00000648803.1:n.51+3436G>T

Variant summary

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

The ENST00000648803.1(ENSG00000234275):​n.51+3436G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.854 in 152,150 control chromosomes in the GnomAD database, including 55,731 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 0.85 (55731 hom., cov: 31)
• Consequence: ENSG00000234275 ENST00000648803.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.10
• Publications: 5 publications found

Genes affected

ENSG00000234275 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.53).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.973 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000234275	ENST00000648803.1	n.51+3436G>T		intron_variant	Intron 1 of 7
ENSG00000234275	ENST00000650957.2	n.57+3436G>T		intron_variant	Intron 1 of 5

Frequencies

GnomAD3 genomes AF: 0.854 AC: 129874 AN: 152032 Hom.: 55678 Cov.: 31

Gnomad AFR AF: 0.886

Gnomad AMI AF: 0.759

Gnomad AMR AF: 0.889

Gnomad ASJ AF: 0.902

Gnomad EAS AF: 0.996

Gnomad SAS AF: 0.934

Gnomad FIN AF: 0.844

Gnomad MID AF: 0.889

Gnomad NFE AF: 0.810

Gnomad OTH AF: 0.868

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

GnomAD4 genome AF: 0.854 AC: 129985 AN: 152150 Hom.: 55731 Cov.: 31 AF XY: 0.859 AC XY: 63906 AN XY: 74368

African (AFR) AF: 0.886 AC: 36787 AN: 41502

American (AMR) AF: 0.889 AC: 13594 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.902 AC: 3133 AN: 3472

East Asian (EAS) AF: 0.996 AC: 5139 AN: 5162

South Asian (SAS) AF: 0.934 AC: 4501 AN: 4818

European-Finnish (FIN) AF: 0.844 AC: 8944 AN: 10596

Middle Eastern (MID) AF: 0.881 AC: 259 AN: 294

European-Non Finnish (NFE) AF: 0.810 AC: 55102 AN: 67994

Other (OTH) AF: 0.868 AC: 1834 AN: 2112

Alfa AF: 0.831 Hom.: 168244

Bravo AF: 0.857

Asia WGS AF: 0.950 AC: 3302 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.53
CADD	Benign	15
DANN	Benign	0.61
PhyloP100		2.1

Splicing

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

Other links and lift over

dbSNP: rs4669060; hg19: chr2-6478428;