rs723815

Variant names:

• chr6-52654405-C-A
• rs723815
• ENST00000847779.1:n.126+1827G>T

Variant summary

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

The ENST00000847779.1(ENSG00000310175):​n.126+1827G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.195 in 152,008 control chromosomes in the GnomAD database, including 3,007 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 0.19 (3007 hom., cov: 32)
• Consequence: ENSG00000310175 ENST00000847779.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.305
• Publications: 5 publications found

Genes affected

ENSG00000310175 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.263 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
ENSG00000310175	ENST00000847779.1	n.126+1827G>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.195 AC: 29607 AN: 151890 Hom.: 3003 Cov.: 32

Gnomad AFR AF: 0.267

Gnomad AMI AF: 0.260

Gnomad AMR AF: 0.160

Gnomad ASJ AF: 0.195

Gnomad EAS AF: 0.146

Gnomad SAS AF: 0.248

Gnomad FIN AF: 0.125

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.168

Gnomad OTH AF: 0.202

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

GnomAD4 genome AF: 0.195 AC: 29629 AN: 152008 Hom.: 3007 Cov.: 32 AF XY: 0.191 AC XY: 14184 AN XY: 74304

African (AFR) AF: 0.267 AC: 11078 AN: 41460

American (AMR) AF: 0.160 AC: 2449 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.195 AC: 676 AN: 3472

East Asian (EAS) AF: 0.146 AC: 757 AN: 5186

South Asian (SAS) AF: 0.249 AC: 1199 AN: 4816

European-Finnish (FIN) AF: 0.125 AC: 1315 AN: 10544

Middle Eastern (MID) AF: 0.224 AC: 65 AN: 290

European-Non Finnish (NFE) AF: 0.168 AC: 11427 AN: 67946

Other (OTH) AF: 0.202 AC: 426 AN: 2114

Alfa AF: 0.179 Hom.: 9822

Bravo AF: 0.199

Asia WGS AF: 0.197 AC: 686 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.34
DANN	Benign	0.28
PhyloP100		-0.30

Splicing

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

Other links and lift over

dbSNP: rs723815; hg19: chr6-52519203;