ENST00000744920.1:n.121-1945A>G

Variant names:

• chr6-31394060-A-G
• rs10947208
• ENST00000744920.1:n.121-1945A>G

Variant summary

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

The ENST00000744920.1(ENSG00000297040):​n.121-1945A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.307 in 151,002 control chromosomes in the GnomAD database, including 7,528 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 0.31 (7528 hom., cov: 31)
• Consequence: ENSG00000297040 ENST00000744920.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0920
• Publications: 12 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=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.352 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MICA-AS1	NR_148222.1	n.*229T>C		downstream_gene_variant
MICA-AS1	NR_148223.1	n.*229T>C		downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000297040	ENST00000744920.1	n.121-1945A>G		intron_variant	Intron 1 of 2
MICA-AS1	ENST00000745027.1	n.567+5994T>C		intron_variant	Intron 1 of 1
MICA-AS1	ENST00000606743.1	n.*229T>C		downstream_gene_variant		6

Frequencies

GnomAD3 genomes AF: 0.307 AC: 46286 AN: 150886 Hom.: 7513 Cov.: 31

Gnomad AFR AF: 0.357

Gnomad AMI AF: 0.468

Gnomad AMR AF: 0.349

Gnomad ASJ AF: 0.557

Gnomad EAS AF: 0.311

Gnomad SAS AF: 0.303

Gnomad FIN AF: 0.333

Gnomad MID AF: 0.345

Gnomad NFE AF: 0.248

Gnomad OTH AF: 0.316

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

GnomAD4 genome AF: 0.307 AC: 46344 AN: 151002 Hom.: 7528 Cov.: 31 AF XY: 0.312 AC XY: 23054 AN XY: 73824

African (AFR) AF: 0.357 AC: 14586 AN: 40866

American (AMR) AF: 0.350 AC: 5260 AN: 15044

Ashkenazi Jewish (ASJ) AF: 0.557 AC: 1912 AN: 3432

East Asian (EAS) AF: 0.311 AC: 1593 AN: 5122

South Asian (SAS) AF: 0.302 AC: 1452 AN: 4804

European-Finnish (FIN) AF: 0.333 AC: 3512 AN: 10534

Middle Eastern (MID) AF: 0.344 AC: 99 AN: 288

European-Non Finnish (NFE) AF: 0.248 AC: 16833 AN: 67912

Other (OTH) AF: 0.322 AC: 675 AN: 2098

Alfa AF: 0.275 Hom.: 3997

Asia WGS AF: 0.316 AC: 1099 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	4.1
DANN	Benign	0.71
PhyloP100		0.092

Splicing

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

Other links and lift over

dbSNP: rs10947208; hg19: chr6-31361837;