rs320813

Variant names:

• chr7-9745624-G-A
• rs320813
• ENST00000447999.2:n.1026+2322G>A

Variant summary

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

The ENST00000447999.2(ENSG00000234710):​n.1026+2322G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.301 in 151,804 control chromosomes in the GnomAD database, including 7,311 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 (7311 hom., cov: 33)
• Consequence: ENSG00000234710 ENST00000447999.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.466
• Publications: 1 publications found

Genes affected

ENSG00000234710 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.348 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105375148	NR_187872.1	n.479+2322G>A		intron_variant	Intron 4 of 5
LOC105375148	NR_187873.1	n.1990+2322G>A		intron_variant	Intron 7 of 8
LOC105375148	NR_187874.1	n.1930+2322G>A		intron_variant	Intron 6 of 7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000234710	ENST00000447999.2	n.1026+2322G>A		intron_variant	Intron 7 of 8	3
ENSG00000234710	ENST00000657272.2	n.520+2322G>A		intron_variant	Intron 4 of 5
ENSG00000234710	ENST00000668655.1	n.495+2322G>A		intron_variant	Intron 4 of 6

Frequencies

GnomAD3 genomes AF: 0.301 AC: 45635 AN: 151686 Hom.: 7309 Cov.: 33

Gnomad AFR AF: 0.192

Gnomad AMI AF: 0.438

Gnomad AMR AF: 0.308

Gnomad ASJ AF: 0.308

Gnomad EAS AF: 0.342

Gnomad SAS AF: 0.295

Gnomad FIN AF: 0.351

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.352

Gnomad OTH AF: 0.323

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

GnomAD4 genome AF: 0.301 AC: 45646 AN: 151804 Hom.: 7311 Cov.: 33 AF XY: 0.301 AC XY: 22337 AN XY: 74188

African (AFR) AF: 0.191 AC: 7934 AN: 41472

American (AMR) AF: 0.308 AC: 4694 AN: 15222

Ashkenazi Jewish (ASJ) AF: 0.308 AC: 1068 AN: 3466

East Asian (EAS) AF: 0.342 AC: 1752 AN: 5126

South Asian (SAS) AF: 0.297 AC: 1434 AN: 4830

European-Finnish (FIN) AF: 0.351 AC: 3707 AN: 10552

Middle Eastern (MID) AF: 0.381 AC: 112 AN: 294

European-Non Finnish (NFE) AF: 0.352 AC: 23873 AN: 67826

Other (OTH) AF: 0.320 AC: 673 AN: 2104

Alfa AF: 0.323 Hom.: 2984

Bravo AF: 0.296

Asia WGS AF: 0.289 AC: 1006 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.0
DANN	Benign	0.48
PhyloP100		-0.47

Splicing

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

Other links and lift over

dbSNP: rs320813; hg19: chr7-9785253;