rs6860577

Positions:

• chr5-165440015-G-T

Variant summary

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

The ENST00000522189.1(ENSG00000253693):​n.21+90965G>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 0.328 in 152,116 control chromosomes in the GnomAD database, including 8,435 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 0.33 (8435 hom., cov: 33)
• Consequence: ENST00000522189.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.654

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.381 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000522189.1	n.21+90965G>T		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.328 AC: 49801 AN: 151998 Hom.: 8432 Cov.: 33

Gnomad AFR AF: 0.386

Gnomad AMI AF: 0.233

Gnomad AMR AF: 0.285

Gnomad ASJ AF: 0.328

Gnomad EAS AF: 0.146

Gnomad SAS AF: 0.276

Gnomad FIN AF: 0.295

Gnomad MID AF: 0.405

Gnomad NFE AF: 0.325

Gnomad OTH AF: 0.330

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

GnomAD4 genome AF: 0.328 AC: 49819 AN: 152116 Hom.: 8435 Cov.: 33 AF XY: 0.324 AC XY: 24117 AN XY: 74388

Gnomad4 AFR AF: 0.386

Gnomad4 AMR AF: 0.284

Gnomad4 ASJ AF: 0.328

Gnomad4 EAS AF: 0.146

Gnomad4 SAS AF: 0.276

Gnomad4 FIN AF: 0.295

Gnomad4 NFE AF: 0.325

Gnomad4 OTH AF: 0.327

Alfa AF: 0.329 Hom.: 1721

Bravo AF: 0.327

Asia WGS AF: 0.208 AC: 727 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	6.1
DANN	Benign	0.86

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6860577; hg19: chr5-164867020;