6-31384854-A-G

Variant names:

• chr6-31384854-A-G
• rs7741091
• ENST00000745027.1:n.568-1664T>C

Variant summary

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

The ENST00000745027.1(MICA-AS1):​n.568-1664T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.36 in 151,468 control chromosomes in the GnomAD database, including 10,257 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 0.36 (10257 hom., cov: 32)
• Consequence: MICA-AS1 ENST00000745027.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.211
• Publications: 29 publications found

Genes affected

MICA-AS1 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.415 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000745027.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MICA-AS1	ENST00000745027.1		n.568-1664T>C		intron	N/A
	MICA-AS1	ENST00000745028.1		n.331-1664T>C		intron	N/A
	MICA-AS1	ENST00000745029.1		n.232+58T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.360 AC: 54447 AN: 151346 Hom.: 10244 Cov.: 32

Gnomad AFR AF: 0.379

Gnomad AMI AF: 0.510

Gnomad AMR AF: 0.423

Gnomad ASJ AF: 0.605

Gnomad EAS AF: 0.319

Gnomad SAS AF: 0.415

Gnomad FIN AF: 0.400

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.311

Gnomad OTH AF: 0.390

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

GnomAD4 genome AF: 0.360 AC: 54505 AN: 151468 Hom.: 10257 Cov.: 32 AF XY: 0.366 AC XY: 27069 AN XY: 74052

African (AFR) AF: 0.379 AC: 15632 AN: 41198

American (AMR) AF: 0.424 AC: 6434 AN: 15192

Ashkenazi Jewish (ASJ) AF: 0.605 AC: 2085 AN: 3446

East Asian (EAS) AF: 0.320 AC: 1648 AN: 5158

South Asian (SAS) AF: 0.416 AC: 1991 AN: 4790

European-Finnish (FIN) AF: 0.400 AC: 4230 AN: 10564

Middle Eastern (MID) AF: 0.445 AC: 129 AN: 290

European-Non Finnish (NFE) AF: 0.311 AC: 21070 AN: 67830

Other (OTH) AF: 0.393 AC: 822 AN: 2090

Alfa AF: 0.333 Hom.: 22434

Bravo AF: 0.363

Asia WGS AF: 0.349 AC: 1216 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	11
DANN	Benign	0.64
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs7741091; hg19: chr6-31352631;