rs66609536

Variant names:

• chr6-31394343-G-A
• rs66609536
• ENST00000606743.1:n.1153C>T

Variant summary

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

The ENST00000606743.1(MICA-AS1):​n.1153C>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 ENST00000606743.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.391
• Publications: 6 publications found

Genes affected

MICA-AS1 (HGNC:):

MICA-AS1 (HGNC:53631): (MICA antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
MICA-AS1	NR_148222.1	n.1292C>T		non_coding_transcript_exon_variant	Exon 2 of 2
MICA-AS1	NR_148223.1	n.1325C>T		non_coding_transcript_exon_variant	Exon 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MICA-AS1	ENST00000606743.1	n.1153C>T		non_coding_transcript_exon_variant	Exon 1 of 1	6
MICA-AS1	ENST00000745010.1	n.1615C>T		non_coding_transcript_exon_variant	Exon 2 of 2
MICA-AS1	ENST00000745011.1	n.1552C>T		non_coding_transcript_exon_variant	Exon 3 of 3

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.367 AC: 14807 AN: 40316

American (AMR) AF: 0.358 AC: 5359 AN: 14952

Ashkenazi Jewish (ASJ) AF: 0.558 AC: 1921 AN: 3444

East Asian (EAS) AF: 0.314 AC: 1607 AN: 5116

South Asian (SAS) AF: 0.305 AC: 1451 AN: 4754

European-Finnish (FIN) AF: 0.336 AC: 3532 AN: 10518

Middle Eastern (MID) AF: 0.350 AC: 100 AN: 286

European-Non Finnish (NFE) AF: 0.249 AC: 16877 AN: 67780

Other (OTH) AF: 0.326 AC: 682 AN: 2092

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
PhyloP100		0.39

Splicing

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

Other links and lift over

dbSNP: rs66609536; hg19: chr6-31362120;