rs500192

Variant names:

• chr6-127659577-G-T
• rs500192

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

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: LOC100421513 intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.31
• Publications: 3 publications found

Genes affected

LOC100421513 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000568952.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000260212	ENST00000568952.1	TSL:6	n.33+121G>T		intron	N/A
	ENSG00000305799	ENST00000813004.1		n.319+27260G>T		intron	N/A
	ENSG00000305799	ENST00000813005.1		n.192-31946G>T		intron	N/A

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

African (AFR) AF: 0.103 AC: 1511 AN: 14670

American (AMR) AF: 0.194 AC: 5251 AN: 27062

Ashkenazi Jewish (ASJ) AF: 0.376 AC: 5696 AN: 15150

East Asian (EAS) AF: 0.000798 AC: 26 AN: 32582

South Asian (SAS) AF: 0.183 AC: 9966 AN: 54596

European-Finnish (FIN) AF: 0.407 AC: 17611 AN: 43262

Middle Eastern (MID) AF: 0.351 AC: 723 AN: 2062

European-Non Finnish (NFE) AF: 0.432 AC: 134820 AN: 311814

Other (OTH) AF: 0.343 AC: 9593 AN: 27940

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

African (AFR) AF: 0.104 AC: 4325 AN: 41454

American (AMR) AF: 0.249 AC: 3793 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.383 AC: 1329 AN: 3470

East Asian (EAS) AF: 0.00330 AC: 17 AN: 5158

South Asian (SAS) AF: 0.174 AC: 835 AN: 4810

European-Finnish (FIN) AF: 0.422 AC: 4454 AN: 10558

Middle Eastern (MID) AF: 0.340 AC: 100 AN: 294

European-Non Finnish (NFE) AF: 0.440 AC: 29891 AN: 67940

Other (OTH) AF: 0.302 AC: 637 AN: 2112

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.55
CADD	Benign	19
DANN	Benign	0.84
PhyloP100		1.3

Splicing

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

Other links and lift over

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