6-31394533-C-T

Position:

• chr6-31394533-C-T

Variant summary

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

The NR_148222.1(MICA-AS1):​n.1102G>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 NR_148222.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.03

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MICA-AS1	NR_148222.1	n.1102G>A		non_coding_transcript_exon_variant	2/2
MICA-AS1	NR_148223.1	n.1135G>A		non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000606743.1	n.963G>A		non_coding_transcript_exon_variant	1/1

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

Gnomad4 ASJ exome AF: 0.00

Gnomad4 SAS exome AF: 0.500

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.300

Gnomad4 OTH exome AF: 0.00

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

Gnomad4 AFR AF: 0.167

Gnomad4 AMR AF: 0.144

Gnomad4 ASJ AF: 0.0764

Gnomad4 EAS AF: 0.0278

Gnomad4 SAS AF: 0.103

Gnomad4 FIN AF: 0.00777

Gnomad4 NFE AF: 0.0798

Gnomad4 OTH AF: 0.144

Alfa AF: 0.0854 Hom.: 114

Bravo AF: 0.118

Asia WGS AF: 0.0700 AC: 241 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.6
DANN	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16899524; hg19: chr6-31362310;