rs2251396

Variant names:

• chr6-31396930-G-A
• rs2251396
• ENST00000744920.1:n.181-176G>A

Your query was ambiguous. Multiple possible variants found:

• chr6-31396930-G-A
• chr6-31396930-G-C
• chr6-31396930-G-T

Variant summary

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

The ENST00000744920.1(ENSG00000297040):​n.181-176G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.242 in 151,840 control chromosomes in the GnomAD database, including 4,928 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 0.24 (4928 hom., cov: 33)
• Consequence: ENSG00000297040 ENST00000744920.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.567
• Publications: 46 publications found

Genes affected

ENSG00000297040 (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=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.291 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000744920.1. 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.418-1713C>T		intron	N/A
	MICA-AS1	NR_148223.1		n.450+1129C>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000297040	ENST00000744920.1		n.181-176G>A		intron	N/A
	MICA-AS1	ENST00000745010.1		n.741-1713C>T		intron	N/A
	MICA-AS1	ENST00000745011.1		n.677+1129C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.242 AC: 36705 AN: 151722 Hom.: 4930 Cov.: 33

Gnomad AFR AF: 0.183

Gnomad AMI AF: 0.313

Gnomad AMR AF: 0.178

Gnomad ASJ AF: 0.123

Gnomad EAS AF: 0.275

Gnomad SAS AF: 0.182

Gnomad FIN AF: 0.279

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.294

Gnomad OTH AF: 0.206

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

GnomAD4 genome AF: 0.242 AC: 36715 AN: 151840 Hom.: 4928 Cov.: 33 AF XY: 0.238 AC XY: 17675 AN XY: 74244

African (AFR) AF: 0.183 AC: 7584 AN: 41366

American (AMR) AF: 0.178 AC: 2706 AN: 15198

Ashkenazi Jewish (ASJ) AF: 0.123 AC: 426 AN: 3460

East Asian (EAS) AF: 0.275 AC: 1416 AN: 5156

South Asian (SAS) AF: 0.183 AC: 882 AN: 4820

European-Finnish (FIN) AF: 0.279 AC: 2950 AN: 10568

Middle Eastern (MID) AF: 0.153 AC: 45 AN: 294

European-Non Finnish (NFE) AF: 0.294 AC: 19989 AN: 67958

Other (OTH) AF: 0.205 AC: 432 AN: 2108

Alfa AF: 0.278 Hom.: 20970

Bravo AF: 0.233

Asia WGS AF: 0.195 AC: 680 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.2
DANN	Benign	0.47
PhyloP100		-0.57

Splicing

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

Other links and lift over

dbSNP: rs2251396; hg19: chr6-31364707;