6-31398010-G-A

Variant names:

• chr6-31398010-G-A
• rs4349859
• ENST00000745010.1:n.740+2044C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000745010.1(MICA-AS1):​n.740+2044C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0306 in 152,092 control chromosomes in the GnomAD database, including 120 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 0.031 (120 hom., cov: 33)
• Consequence: MICA-AS1 ENST00000745010.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.208
• Publications: 44 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=-0.86).
• BS1: Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.0306 (4650/152092) while in subpopulation NFE AF = 0.0443 (3010/68002). AF 95% confidence interval is 0.0429. There are 120 homozygotes in GnomAd4. There are 2342 alleles in the male GnomAd4 subpopulation. Median coverage is 33. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 120 gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000745010.1. 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.417+2044C>T		intron	N/A
	MICA-AS1	NR_148223.1		n.450+49C>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MICA-AS1	ENST00000745010.1		n.740+2044C>T		intron	N/A
	MICA-AS1	ENST00000745011.1		n.677+49C>T		intron	N/A
	MICA-AS1	ENST00000745012.1		n.839+780C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0306 AC: 4649 AN: 151974 Hom.: 120 Cov.: 33

Gnomad AFR AF: 0.00740

Gnomad AMI AF: 0.0319

Gnomad AMR AF: 0.0180

Gnomad ASJ AF: 0.0171

Gnomad EAS AF: 0.00481

Gnomad SAS AF: 0.0164

Gnomad FIN AF: 0.0779

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0443

Gnomad OTH AF: 0.0192

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0306 AC: 4650 AN: 152092 Hom.: 120 Cov.: 33 AF XY: 0.0315 AC XY: 2342 AN XY: 74380

African (AFR) AF: 0.00742 AC: 308 AN: 41484

American (AMR) AF: 0.0180 AC: 274 AN: 15224

Ashkenazi Jewish (ASJ) AF: 0.0171 AC: 59 AN: 3460

East Asian (EAS) AF: 0.00482 AC: 25 AN: 5182

South Asian (SAS) AF: 0.0164 AC: 79 AN: 4824

European-Finnish (FIN) AF: 0.0779 AC: 826 AN: 10604

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.0443 AC: 3010 AN: 68002

Other (OTH) AF: 0.0190 AC: 40 AN: 2108

Alfa AF: 0.0373 Hom.: 452

Bravo AF: 0.0256

Asia WGS AF: 0.0180 AC: 61 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.1
DANN	Benign	0.72
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs4349859; hg19: chr6-31365787;