rs969088

Positions:

• chr5-26389153-G-C
• chr5-26389153-G-T

Variant summary

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

The ENST00000512939.1(ENSG00000249099):​n.227+447C>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 0.0994 in 152,182 control chromosomes in the GnomAD database, including 1,295 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 0.099 (1295 hom., cov: 32)
• Consequence: ENST00000512939.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.810

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.247 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
	ENST00000512939.1	n.227+447C>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.0991 AC: 15076 AN: 152064 Hom.: 1282 Cov.: 32

Gnomad AFR AF: 0.206

Gnomad AMI AF: 0.00440

Gnomad AMR AF: 0.135

Gnomad ASJ AF: 0.0576

Gnomad EAS AF: 0.259

Gnomad SAS AF: 0.0804

Gnomad FIN AF: 0.0295

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0299

Gnomad OTH AF: 0.0946

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

GnomAD4 genome AF: 0.0994 AC: 15129 AN: 152182 Hom.: 1295 Cov.: 32 AF XY: 0.101 AC XY: 7499 AN XY: 74386

Gnomad4 AFR AF: 0.206

Gnomad4 AMR AF: 0.135

Gnomad4 ASJ AF: 0.0576

Gnomad4 EAS AF: 0.259

Gnomad4 SAS AF: 0.0792

Gnomad4 FIN AF: 0.0295

Gnomad4 NFE AF: 0.0299

Gnomad4 OTH AF: 0.102

Alfa AF: 0.0635 Hom.: 95

Bravo AF: 0.114

Asia WGS AF: 0.168 AC: 588 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	4.1
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs969088; hg19: chr5-26389262;