rs6924962

Variant names:

• chr6-31390525-T-C
• rs6924962
• ENST00000744920.1:n.120+1084T>C

Your query was ambiguous. Multiple possible variants found:

• chr6-31390525-T-C
• chr6-31390525-T-G

Variant summary

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

The ENST00000744920.1(ENSG00000297040):​n.120+1084T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.25 in 146,938 control chromosomes in the GnomAD database, including 3,509 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 0.25 (3509 hom., cov: 29)
• Consequence: ENSG00000297040 ENST00000744920.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.672
• Publications: 5 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=-1.04).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.299 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000297040	ENST00000744920.1		n.120+1084T>C		intron	N/A
	ENSG00000297040	ENST00000744921.1		n.91+1084T>C		intron	N/A
	MICA-AS1	ENST00000745027.1		n.568-7335A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.250 AC: 36681 AN: 146816 Hom.: 3494 Cov.: 29

Gnomad AFR AF: 0.303

Gnomad AMI AF: 0.290

Gnomad AMR AF: 0.303

Gnomad ASJ AF: 0.416

Gnomad EAS AF: 0.217

Gnomad SAS AF: 0.214

Gnomad FIN AF: 0.301

Gnomad MID AF: 0.271

Gnomad NFE AF: 0.194

Gnomad OTH AF: 0.261

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

GnomAD4 genome AF: 0.250 AC: 36737 AN: 146938 Hom.: 3509 Cov.: 29 AF XY: 0.254 AC XY: 18177 AN XY: 71656

African (AFR) AF: 0.303 AC: 12091 AN: 39872

American (AMR) AF: 0.303 AC: 4397 AN: 14500

Ashkenazi Jewish (ASJ) AF: 0.416 AC: 1368 AN: 3286

East Asian (EAS) AF: 0.217 AC: 1064 AN: 4896

South Asian (SAS) AF: 0.214 AC: 991 AN: 4628

European-Finnish (FIN) AF: 0.301 AC: 3049 AN: 10142

Middle Eastern (MID) AF: 0.268 AC: 76 AN: 284

European-Non Finnish (NFE) AF: 0.194 AC: 12907 AN: 66422

Other (OTH) AF: 0.266 AC: 540 AN: 2032

Alfa AF: 0.0851 Hom.: 73

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.4
DANN	Benign	0.11
PhyloP100		-0.67

Splicing

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

Other links and lift over

dbSNP: rs6924962; hg19: chr6-31358302;