chr6-31392318-G-A

Variant names:

• chr6-31392318-G-A
• rs2596517
• ENST00000744920.1:n.120+2877G>A

Variant summary

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

The ENST00000744920.1(ENSG00000297040):​n.120+2877G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.848 in 151,740 control chromosomes in the GnomAD database, including 54,869 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 0.85 (54869 hom., cov: 32)
• Consequence: ENSG00000297040 ENST00000744920.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.25
• Publications: 8 publications found

Genes affected

ENSG00000297040 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.929 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000297040	ENST00000744920.1		n.120+2877G>A		intron	N/A
	ENSG00000297040	ENST00000744921.1		n.92-67G>A		intron	N/A
	MICA-AS1	ENST00000745027.1		n.567+7736C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.848 AC: 128638 AN: 151624 Hom.: 54817 Cov.: 32

Gnomad AFR AF: 0.830

Gnomad AMI AF: 0.922

Gnomad AMR AF: 0.898

Gnomad ASJ AF: 0.930

Gnomad EAS AF: 0.951

Gnomad SAS AF: 0.940

Gnomad FIN AF: 0.840

Gnomad MID AF: 0.927

Gnomad NFE AF: 0.829

Gnomad OTH AF: 0.880

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

GnomAD4 genome AF: 0.848 AC: 128745 AN: 151740 Hom.: 54869 Cov.: 32 AF XY: 0.852 AC XY: 63197 AN XY: 74146

African (AFR) AF: 0.830 AC: 34228 AN: 41214

American (AMR) AF: 0.899 AC: 13653 AN: 15194

Ashkenazi Jewish (ASJ) AF: 0.930 AC: 3218 AN: 3460

East Asian (EAS) AF: 0.951 AC: 4915 AN: 5166

South Asian (SAS) AF: 0.940 AC: 4523 AN: 4812

European-Finnish (FIN) AF: 0.840 AC: 8884 AN: 10582

Middle Eastern (MID) AF: 0.925 AC: 272 AN: 294

European-Non Finnish (NFE) AF: 0.829 AC: 56351 AN: 67998

Other (OTH) AF: 0.882 AC: 1860 AN: 2108

Alfa AF: 0.833 Hom.: 7442

Bravo AF: 0.850

Asia WGS AF: 0.936 AC: 3252 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	5.4
DANN	Benign	0.48
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs2596517; hg19: chr6-31360095;