rs500192

Positions:

• chr6-127659577-G-T

Variant summary

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

The ENST00000568952.1(ENSG00000260212):​n.33+121G>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 0.339 in 681,094 control chromosomes in the GnomAD database, including 46,485 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 0.30 (8881 hom., cov: 30)
  • Exomes 𝑓: 0.35 (37604 hom.)
• Consequence: ENST00000568952.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.31

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.55).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.436 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
	ENST00000568952.1	n.33+121G>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.302 AC: 45797 AN: 151836 Hom.: 8883 Cov.: 30

Gnomad AFR AF: 0.104

Gnomad AMI AF: 0.451

Gnomad AMR AF: 0.249

Gnomad ASJ AF: 0.383

Gnomad EAS AF: 0.00329

Gnomad SAS AF: 0.174

Gnomad FIN AF: 0.422

Gnomad MID AF: 0.350

Gnomad NFE AF: 0.440

Gnomad OTH AF: 0.305

GnomAD4 exome AF: 0.350 AC: 185197 AN: 529138 Hom.: 37604 Cov.: 6 AF XY: 0.346 AC XY: 98208 AN XY: 284236

Gnomad4 AFR exome AF: 0.103

Gnomad4 AMR exome AF: 0.194

Gnomad4 ASJ exome AF: 0.376

Gnomad4 EAS exome AF: 0.000798

Gnomad4 SAS exome AF: 0.183

Gnomad4 FIN exome AF: 0.407

Gnomad4 NFE exome AF: 0.432

Gnomad4 OTH exome AF: 0.343

GnomAD4 genome AF: 0.301 AC: 45790 AN: 151956 Hom.: 8881 Cov.: 30 AF XY: 0.296 AC XY: 21978 AN XY: 74272

Gnomad4 AFR AF: 0.104

Gnomad4 AMR AF: 0.249

Gnomad4 ASJ AF: 0.383

Gnomad4 EAS AF: 0.00330

Gnomad4 SAS AF: 0.174

Gnomad4 FIN AF: 0.422

Gnomad4 NFE AF: 0.440

Gnomad4 OTH AF: 0.302

Alfa AF: 0.341 Hom.: 1714

Bravo AF: 0.278

Asia WGS AF: 0.0840 AC: 294 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.55
CADD	Benign	19
DANN	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs500192; hg19: chr6-127980722; COSMIC: COSV68279607;