rs312707

Variant names:

• chr17-70304495-C-A
• rs312707
• ENST00000771979.1:n.146-459C>A

Variant summary

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

The ENST00000771979.1(ENSG00000300458):​n.146-459C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.267 in 151,998 control chromosomes in the GnomAD database, including 5,665 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 0.27 (5665 hom., cov: 31)
• Consequence: ENSG00000300458 ENST00000771979.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.536
• Publications: 4 publications found

Genes affected

ENSG00000300458 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.307 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000771979.1. 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
	ENSG00000300458	ENST00000771979.1		n.146-459C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.268 AC: 40654 AN: 151882 Hom.: 5665 Cov.: 31

Gnomad AFR AF: 0.233

Gnomad AMI AF: 0.145

Gnomad AMR AF: 0.304

Gnomad ASJ AF: 0.195

Gnomad EAS AF: 0.321

Gnomad SAS AF: 0.286

Gnomad FIN AF: 0.413

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.259

Gnomad OTH AF: 0.244

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

GnomAD4 genome AF: 0.267 AC: 40653 AN: 151998 Hom.: 5665 Cov.: 31 AF XY: 0.274 AC XY: 20385 AN XY: 74284

African (AFR) AF: 0.233 AC: 9665 AN: 41482

American (AMR) AF: 0.304 AC: 4643 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.195 AC: 675 AN: 3466

East Asian (EAS) AF: 0.320 AC: 1648 AN: 5148

South Asian (SAS) AF: 0.286 AC: 1381 AN: 4824

European-Finnish (FIN) AF: 0.413 AC: 4356 AN: 10544

Middle Eastern (MID) AF: 0.139 AC: 41 AN: 294

European-Non Finnish (NFE) AF: 0.259 AC: 17604 AN: 67956

Other (OTH) AF: 0.241 AC: 508 AN: 2108

Alfa AF: 0.257 Hom.: 960

Bravo AF: 0.258

Asia WGS AF: 0.251 AC: 875 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.81
DANN	Benign	0.42
PhyloP100		-0.54

Splicing

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

Other links and lift over

dbSNP: rs312707; hg19: chr17-68300636;