rs6920648

Variant names:

• chr6-52143818-A-G
• rs6920648
• ENST00000784740.1:n.121-5046A>G

Variant summary

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

The ENST00000784740.1(ENSG00000302165):​n.121-5046A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.387 in 151,908 control chromosomes in the GnomAD database, including 12,047 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 0.39 (12047 hom., cov: 31)
• Consequence: ENSG00000302165 ENST00000784740.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.860
• Publications: 12 publications found

Genes affected

ENSG00000302165 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.55).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.45 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000302165	ENST00000784740.1	n.121-5046A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.387 AC: 58730 AN: 151790 Hom.: 12047 Cov.: 31

Gnomad AFR AF: 0.339

Gnomad AMI AF: 0.381

Gnomad AMR AF: 0.292

Gnomad ASJ AF: 0.423

Gnomad EAS AF: 0.0854

Gnomad SAS AF: 0.283

Gnomad FIN AF: 0.470

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.454

Gnomad OTH AF: 0.387

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

GnomAD4 genome AF: 0.387 AC: 58735 AN: 151908 Hom.: 12047 Cov.: 31 AF XY: 0.380 AC XY: 28200 AN XY: 74248

African (AFR) AF: 0.338 AC: 14000 AN: 41416

American (AMR) AF: 0.291 AC: 4442 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.423 AC: 1466 AN: 3468

East Asian (EAS) AF: 0.0856 AC: 442 AN: 5164

South Asian (SAS) AF: 0.282 AC: 1358 AN: 4814

European-Finnish (FIN) AF: 0.470 AC: 4957 AN: 10556

Middle Eastern (MID) AF: 0.316 AC: 93 AN: 294

European-Non Finnish (NFE) AF: 0.454 AC: 30825 AN: 67930

Other (OTH) AF: 0.384 AC: 805 AN: 2096

Alfa AF: 0.421 Hom.: 17845

Bravo AF: 0.371

Asia WGS AF: 0.210 AC: 731 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.55
CADD	Benign	11
DANN	Benign	0.61
PhyloP100		0.86

Splicing

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

Other links and lift over

dbSNP: rs6920648; hg19: chr6-52008616;