rs4669060

Positions:

• chr2-6338296-C-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000648803.1(ENSG00000234275):​n.51+3436G>T variant causes a intron, non coding transcript 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: ENST00000648803.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.10

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000648803.1	n.51+3436G>T		intron_variant, non_coding_transcript_variant
	ENST00000650957.2	n.57+3436G>T		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.886

Gnomad4 AMR AF: 0.889

Gnomad4 ASJ AF: 0.902

Gnomad4 EAS AF: 0.996

Gnomad4 SAS AF: 0.934

Gnomad4 FIN AF: 0.844

Gnomad4 NFE AF: 0.810

Gnomad4 OTH AF: 0.868

Alfa AF: 0.826 Hom.: 105288

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4669060; hg19: chr2-6478428;