rs2523471

chr6-31394807-A-G

Variant summary

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

The NR_148222.1(MICA-AS1):n.828T>C 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 0.321 in 129,462 control chromosomes in the GnomAD database, including 8,663 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 0.34 (8623 hom., cov: 24)
  • Exomes 𝑓: 0.084 (40 hom.)
• Consequence: MICA-AS1 NR_148222.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.488

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.454 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MICA-AS1	NR_148222.1	n.828T>C		non_coding_transcript_exon_variant	2/2
MICA-AS1	NR_148223.1	n.861T>C		non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000606743.1	n.689T>C		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.339 AC: 40730 AN: 120060 Hom.: 8601 Cov.: 24

Gnomad AFR AF: 0.459

Gnomad AMI AF: 0.410

Gnomad AMR AF: 0.416

Gnomad ASJ AF: 0.575

Gnomad EAS AF: 0.243

Gnomad SAS AF: 0.319

Gnomad FIN AF: 0.216

Gnomad MID AF: 0.415

Gnomad NFE AF: 0.270

Gnomad OTH AF: 0.399

GnomAD4 exome AF: 0.0840 AC: 782 AN: 9312 Hom.: 40 Cov.: 0 AF XY: 0.0835 AC XY: 376 AN XY: 4504

Gnomad4 AFR exome AF: 0.194

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.0455

Gnomad4 EAS exome AF: 0.0789

Gnomad4 SAS exome AF: 0.112

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.0831

Gnomad4 OTH exome AF: 0.0638

GnomAD4 genome AF: 0.339 AC: 40790 AN: 120150 Hom.: 8623 Cov.: 24 AF XY: 0.335 AC XY: 19441 AN XY: 58054

Gnomad4 AFR AF: 0.460

Gnomad4 AMR AF: 0.417

Gnomad4 ASJ AF: 0.575

Gnomad4 EAS AF: 0.243

Gnomad4 SAS AF: 0.319

Gnomad4 FIN AF: 0.216

Gnomad4 NFE AF: 0.270

Gnomad4 OTH AF: 0.400

Alfa AF: 0.344 Hom.: 1218

Asia WGS AF: 0.376 AC: 1306 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	3.6
Dann	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2523471; hg19: chr6-31362584; COSMIC: COSV74094083;