rs13109195

Positions:

• chr4-145448604-T-C

Variant summary

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

The ENST00000658284.1(ENSG00000286420):​n.255-3168A>G 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 0.0788 in 152,114 control chromosomes in the GnomAD database, including 536 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 0.079 (536 hom., cov: 31)
• Consequence: ENST00000658284.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.966

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.124 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
	ENST00000658284.1	n.255-3168A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0788 AC: 11974 AN: 151996 Hom.: 536 Cov.: 31

Gnomad AFR AF: 0.0820

Gnomad AMI AF: 0.00768

Gnomad AMR AF: 0.0898

Gnomad ASJ AF: 0.0720

Gnomad EAS AF: 0.0873

Gnomad SAS AF: 0.133

Gnomad FIN AF: 0.0663

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.0725

Gnomad OTH AF: 0.0869

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

GnomAD4 genome AF: 0.0788 AC: 11980 AN: 152114 Hom.: 536 Cov.: 31 AF XY: 0.0796 AC XY: 5920 AN XY: 74346

Gnomad4 AFR AF: 0.0821

Gnomad4 AMR AF: 0.0896

Gnomad4 ASJ AF: 0.0720

Gnomad4 EAS AF: 0.0871

Gnomad4 SAS AF: 0.132

Gnomad4 FIN AF: 0.0663

Gnomad4 NFE AF: 0.0725

Gnomad4 OTH AF: 0.0874

Alfa AF: 0.0751 Hom.: 631

Bravo AF: 0.0779

Asia WGS AF: 0.119 AC: 415 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	7.7
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13109195; hg19: chr4-146369756;