6-31395153-C-T

Variant names:

• chr6-31395153-C-T
• rs2523467
• ENST00000606743.1:n.343G>A

Variant summary

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

The NR_148222.1(MICA-AS1):​n.482G>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 0.328 in 955,144 control chromosomes in the GnomAD database, including 56,944 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 0.40 (12824 hom., cov: 26)
  • Exomes 𝑓: 0.32 (44120 hom.)
• Consequence: MICA-AS1 NR_148222.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.05
• Publications: 43 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=-1.06).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.509 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_148222.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MICA-AS1	NR_148222.1		n.482G>A		non_coding_transcript_exon	Exon 2 of 2
	MICA-AS1	NR_148223.1		n.515G>A		non_coding_transcript_exon	Exon 2 of 2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MICA-AS1	ENST00000606743.1	TSL:6	n.343G>A		non_coding_transcript_exon	Exon 1 of 1
	MICA-AS1	ENST00000745010.1		n.805G>A		non_coding_transcript_exon	Exon 2 of 2
	MICA-AS1	ENST00000745011.1		n.742G>A		non_coding_transcript_exon	Exon 3 of 3

Frequencies

GnomAD3 genomes AF: 0.402 AC: 58535 AN: 145622 Hom.: 12801 Cov.: 26

Gnomad AFR AF: 0.515

Gnomad AMI AF: 0.494

Gnomad AMR AF: 0.480

Gnomad ASJ AF: 0.630

Gnomad EAS AF: 0.330

Gnomad SAS AF: 0.394

Gnomad FIN AF: 0.315

Gnomad MID AF: 0.477

Gnomad NFE AF: 0.323

Gnomad OTH AF: 0.456

GnomAD4 exome AF: 0.315 AC: 255015 AN: 809406 Hom.: 44120 Cov.: 31 AF XY: 0.314 AC XY: 117319 AN XY: 373888

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.558 AC: 8601 AN: 15416

American (AMR) AF: 0.551 AC: 529 AN: 960

Ashkenazi Jewish (ASJ) AF: 0.629 AC: 3155 AN: 5018

East Asian (EAS) AF: 0.363 AC: 1291 AN: 3556

South Asian (SAS) AF: 0.399 AC: 6415 AN: 16060

European-Finnish (FIN) AF: 0.310 AC: 83 AN: 268

Middle Eastern (MID) AF: 0.475 AC: 754 AN: 1586

European-Non Finnish (NFE) AF: 0.303 AC: 224558 AN: 740010

Other (OTH) AF: 0.363 AC: 9629 AN: 26532

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

GnomAD4 genome AF: 0.402 AC: 58609 AN: 145738 Hom.: 12824 Cov.: 26 AF XY: 0.402 AC XY: 28543 AN XY: 70934

African (AFR) AF: 0.515 AC: 20092 AN: 38992

American (AMR) AF: 0.481 AC: 6875 AN: 14304

Ashkenazi Jewish (ASJ) AF: 0.630 AC: 2114 AN: 3356

East Asian (EAS) AF: 0.331 AC: 1648 AN: 4986

South Asian (SAS) AF: 0.393 AC: 1806 AN: 4592

European-Finnish (FIN) AF: 0.315 AC: 3061 AN: 9730

Middle Eastern (MID) AF: 0.469 AC: 134 AN: 286

European-Non Finnish (NFE) AF: 0.323 AC: 21521 AN: 66600

Other (OTH) AF: 0.459 AC: 921 AN: 2008

Alfa AF: 0.358 Hom.: 37325

Asia WGS AF: 0.382 AC: 1326 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.94
DANN	Benign	0.28
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs2523467; hg19: chr6-31362930; COSMIC: COSV74094080;