chr6-31394533-C-T

Variant names:

• chr6-31394533-C-T
• rs16899524
• ENST00000606743.1:n.963G>A

Variant summary

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

The ENST00000606743.1(MICA-AS1):​n.963G>A 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 0.104 in 147,466 control chromosomes in the GnomAD database, including 1,106 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 0.10 (1105 hom., cov: 31)
  • Exomes 𝑓: 0.13 (1 hom.)
• Consequence: MICA-AS1 ENST00000606743.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.03
• Publications: 17 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=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.164 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000606743.1. 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
	MICA-AS1	NR_148222.1		n.1102G>A		non_coding_transcript_exon	Exon 2 of 2
	MICA-AS1	NR_148223.1		n.1135G>A		non_coding_transcript_exon	Exon 2 of 2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MICA-AS1	ENST00000606743.1	TSL:6	n.963G>A		non_coding_transcript_exon	Exon 1 of 1
	MICA-AS1	ENST00000745010.1		n.1425G>A		non_coding_transcript_exon	Exon 2 of 2
	MICA-AS1	ENST00000745011.1		n.1362G>A		non_coding_transcript_exon	Exon 3 of 3

Frequencies

GnomAD3 genomes AF: 0.104 AC: 15295 AN: 147318 Hom.: 1102 Cov.: 31

Gnomad AFR AF: 0.167

Gnomad AMI AF: 0.0270

Gnomad AMR AF: 0.144

Gnomad ASJ AF: 0.0764

Gnomad EAS AF: 0.0275

Gnomad SAS AF: 0.103

Gnomad FIN AF: 0.00777

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.0798

Gnomad OTH AF: 0.147

GnomAD4 exome AF: 0.133 AC: 4 AN: 30 Hom.: 1 Cov.: 0 AF XY: 0.250 AC XY: 3 AN XY: 12

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AF: 0.500 AC: 1 AN: 2

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.300 AC: 3 AN: 10

Other (OTH) AF: 0.00 AC: 0 AN: 6

GnomAD4 genome AF: 0.104 AC: 15311 AN: 147436 Hom.: 1105 Cov.: 31 AF XY: 0.101 AC XY: 7230 AN XY: 71908

African (AFR) AF: 0.167 AC: 6561 AN: 39274

American (AMR) AF: 0.144 AC: 2074 AN: 14412

Ashkenazi Jewish (ASJ) AF: 0.0764 AC: 251 AN: 3284

East Asian (EAS) AF: 0.0278 AC: 139 AN: 5006

South Asian (SAS) AF: 0.103 AC: 475 AN: 4614

European-Finnish (FIN) AF: 0.00777 AC: 80 AN: 10290

Middle Eastern (MID) AF: 0.132 AC: 37 AN: 280

European-Non Finnish (NFE) AF: 0.0798 AC: 5373 AN: 67328

Other (OTH) AF: 0.144 AC: 297 AN: 2060

Alfa AF: 0.0851 Hom.: 114

Bravo AF: 0.118

Asia WGS AF: 0.0700 AC: 241 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.6
DANN	Benign	0.34
PhyloP100		-3.0
Mutation Taster		=99/1	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs16899524; hg19: chr6-31362310;