chr6-31387541-T-C

Variant names:

• chr6-31387541-T-C
• rs2596560
• ENST00000745027.1:n.568-4351A>G

Variant summary

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

The ENST00000745027.1(MICA-AS1):​n.568-4351A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.216 in 152,170 control chromosomes in the GnomAD database, including 3,635 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 0.22 (3635 hom., cov: 33)
• Consequence: MICA-AS1 ENST00000745027.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0630
• Publications: 35 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=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.321 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124901300	XR_007059542.1	n.160+193T>C		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MICA-AS1	ENST00000745027.1	n.568-4351A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.216 AC: 32897 AN: 152052 Hom.: 3635 Cov.: 33

Gnomad AFR AF: 0.224

Gnomad AMI AF: 0.164

Gnomad AMR AF: 0.155

Gnomad ASJ AF: 0.167

Gnomad EAS AF: 0.335

Gnomad SAS AF: 0.232

Gnomad FIN AF: 0.215

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.219

Gnomad OTH AF: 0.200

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

GnomAD4 genome AF: 0.216 AC: 32913 AN: 152170 Hom.: 3635 Cov.: 33 AF XY: 0.217 AC XY: 16141 AN XY: 74416

African (AFR) AF: 0.224 AC: 9279 AN: 41500

American (AMR) AF: 0.155 AC: 2369 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.167 AC: 578 AN: 3470

East Asian (EAS) AF: 0.334 AC: 1729 AN: 5170

South Asian (SAS) AF: 0.233 AC: 1126 AN: 4826

European-Finnish (FIN) AF: 0.215 AC: 2285 AN: 10604

Middle Eastern (MID) AF: 0.184 AC: 54 AN: 294

European-Non Finnish (NFE) AF: 0.219 AC: 14921 AN: 67986

Other (OTH) AF: 0.200 AC: 422 AN: 2114

Alfa AF: 0.242 Hom.: 5607

Bravo AF: 0.210

Asia WGS AF: 0.230 AC: 800 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	6.6
DANN	Benign	0.56
PhyloP100		0.063

Splicing

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

Other links and lift over

dbSNP: rs2596560; hg19: chr6-31355318;