rs6466550

Variant names:

• chr7-115675338-T-C
• rs6466550
• ENST00000471672.1:n.210+782A>G

Variant summary

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

The ENST00000471672.1(ENSG00000242072):​n.210+782A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.297 in 151,882 control chromosomes in the GnomAD database, including 8,175 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 0.30 (8175 hom., cov: 32)
• Consequence: ENSG00000242072 ENST00000471672.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.361
• Publications: 1 publications found

Genes affected

ENSG00000242072 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.505 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
ENSG00000242072	ENST00000471672.1	n.210+782A>G		intron_variant	Intron 1 of 1	3

Frequencies

GnomAD3 genomes AF: 0.296 AC: 44990 AN: 151764 Hom.: 8152 Cov.: 32

Gnomad AFR AF: 0.510

Gnomad AMI AF: 0.206

Gnomad AMR AF: 0.244

Gnomad ASJ AF: 0.246

Gnomad EAS AF: 0.357

Gnomad SAS AF: 0.253

Gnomad FIN AF: 0.269

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.185

Gnomad OTH AF: 0.278

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

GnomAD4 genome AF: 0.297 AC: 45065 AN: 151882 Hom.: 8175 Cov.: 32 AF XY: 0.298 AC XY: 22148 AN XY: 74218

African (AFR) AF: 0.510 AC: 21148 AN: 41430

American (AMR) AF: 0.244 AC: 3719 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.246 AC: 855 AN: 3470

East Asian (EAS) AF: 0.357 AC: 1837 AN: 5142

South Asian (SAS) AF: 0.254 AC: 1224 AN: 4822

European-Finnish (FIN) AF: 0.269 AC: 2838 AN: 10550

Middle Eastern (MID) AF: 0.269 AC: 79 AN: 294

European-Non Finnish (NFE) AF: 0.185 AC: 12596 AN: 67918

Other (OTH) AF: 0.275 AC: 581 AN: 2114

Alfa AF: 0.253 Hom.: 800

Bravo AF: 0.305

Asia WGS AF: 0.280 AC: 971 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.1
DANN	Benign	0.37
PhyloP100		-0.36

Splicing

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

Other links and lift over

dbSNP: rs6466550; hg19: chr7-115315392;