7-88610801-G-A

Variant names:

• chr7-88610801-G-A
• rs9632680
• ENST00000663862.1:n.350+70060G>A

Variant summary

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

The ENST00000663862.1(ENSG00000233420):​n.350+70060G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.811 in 152,166 control chromosomes in the GnomAD database, including 50,486 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 0.81 (50442 hom., cov: 31)
  • Exomes 𝑓: 0.84 (44 hom.)
• Consequence: ENSG00000233420 ENST00000663862.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.16
• Publications: 1 publications found

Genes affected

ENSG00000233420 (HGNC:):

SLC66A2P1 (HGNC:43986): (SLC66A2 pseudogene 1)

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 = 0.904 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
ENSG00000233420	ENST00000663862.1	n.350+70060G>A		intron_variant	Intron 3 of 4
SLC66A2P1	ENST00000434950.1	n.-132C>T		upstream_gene_variant		6

Frequencies

GnomAD3 genomes AF: 0.811 AC: 123226 AN: 151924 Hom.: 50376 Cov.: 31

Gnomad AFR AF: 0.912

Gnomad AMI AF: 0.830

Gnomad AMR AF: 0.798

Gnomad ASJ AF: 0.763

Gnomad EAS AF: 0.917

Gnomad SAS AF: 0.745

Gnomad FIN AF: 0.707

Gnomad MID AF: 0.766

Gnomad NFE AF: 0.768

Gnomad OTH AF: 0.808

GnomAD4 exome AF: 0.844 AC: 103 AN: 122 Hom.: 44 AF XY: 0.847 AC XY: 83 AN XY: 98

African (AFR) AF: 1.00 AC: 4 AN: 4

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AF: 1.00 AC: 2 AN: 2

East Asian (EAS) AF: 1.00 AC: 2 AN: 2

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.794 AC: 27 AN: 34

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.846 AC: 66 AN: 78

Other (OTH) AF: 1.00 AC: 2 AN: 2

GnomAD4 genome AF: 0.811 AC: 123351 AN: 152044 Hom.: 50442 Cov.: 31 AF XY: 0.807 AC XY: 59963 AN XY: 74312

African (AFR) AF: 0.912 AC: 37817 AN: 41468

American (AMR) AF: 0.799 AC: 12198 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.763 AC: 2648 AN: 3472

East Asian (EAS) AF: 0.917 AC: 4733 AN: 5160

South Asian (SAS) AF: 0.746 AC: 3589 AN: 4814

European-Finnish (FIN) AF: 0.707 AC: 7462 AN: 10560

Middle Eastern (MID) AF: 0.759 AC: 223 AN: 294

European-Non Finnish (NFE) AF: 0.768 AC: 52215 AN: 67980

Other (OTH) AF: 0.809 AC: 1709 AN: 2112

Alfa AF: 0.763 Hom.: 19535

Bravo AF: 0.827

Asia WGS AF: 0.851 AC: 2958 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.8
DANN	Benign	0.66
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs9632680; hg19: chr7-88240115;