rs66609536

chr6-31394343-G-A

Variant summary

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

The NR_148222.1(MICA-AS1):n.1292C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.311 in 150,168 control chromosomes in the GnomAD database, including 7,838 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 0.31 (7838 hom., cov: 31)
  • Failed GnomAD Quality Control
• Consequence: MICA-AS1 NR_148222.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.391

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.362 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MICA-AS1	NR_148222.1	n.1292C>T		non_coding_transcript_exon_variant	2/2
MICA-AS1	NR_148223.1	n.1325C>T		non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000606743.1	n.1153C>T		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.311 AC: 46705 AN: 150054 Hom.: 7823 Cov.: 31

Gnomad AFR AF: 0.367

Gnomad AMI AF: 0.470

Gnomad AMR AF: 0.358

Gnomad ASJ AF: 0.558

Gnomad EAS AF: 0.314

Gnomad SAS AF: 0.306

Gnomad FIN AF: 0.336

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.249

Gnomad OTH AF: 0.320

GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.311 AC: 46764 AN: 150168 Hom.: 7838 Cov.: 31 AF XY: 0.317 AC XY: 23221 AN XY: 73330

Gnomad4 AFR AF: 0.367

Gnomad4 AMR AF: 0.358

Gnomad4 ASJ AF: 0.558

Gnomad4 EAS AF: 0.314

Gnomad4 SAS AF: 0.305

Gnomad4 FIN AF: 0.336

Gnomad4 NFE AF: 0.249

Gnomad4 OTH AF: 0.326

Alfa AF: 0.277 Hom.: 787

Bravo AF: 0.315

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	4.2
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: rs66609536; hg19: chr6-31362120;