rs9900808

Variant names:

• chr17-13159478-G-A
• rs9900808
• ENST00000835213.1:n.509+3370G>A

Variant summary

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

The ENST00000835213.1(ENSG00000308590):​n.509+3370G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0547 in 152,222 control chromosomes in the GnomAD database, including 308 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 0.055 (308 hom., cov: 32)
• Consequence: ENSG00000308590 ENST00000835213.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.223
• Publications: 6 publications found

Genes affected

ENSG00000308590 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0997 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
ENSG00000308590	ENST00000835213.1	n.509+3370G>A		intron_variant	Intron 3 of 3
ENSG00000308590	ENST00000835214.1	n.362+10614G>A		intron_variant	Intron 2 of 2
ENSG00000308590	ENST00000835215.1	n.571+3370G>A		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.0546 AC: 8308 AN: 152104 Hom.: 306 Cov.: 32

Gnomad AFR AF: 0.102

Gnomad AMI AF: 0.00987

Gnomad AMR AF: 0.0374

Gnomad ASJ AF: 0.0490

Gnomad EAS AF: 0.0596

Gnomad SAS AF: 0.0363

Gnomad FIN AF: 0.00754

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.0387

Gnomad OTH AF: 0.0544

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

GnomAD4 genome AF: 0.0547 AC: 8329 AN: 152222 Hom.: 308 Cov.: 32 AF XY: 0.0531 AC XY: 3954 AN XY: 74422

African (AFR) AF: 0.102 AC: 4244 AN: 41508

American (AMR) AF: 0.0374 AC: 572 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0490 AC: 170 AN: 3468

East Asian (EAS) AF: 0.0597 AC: 309 AN: 5172

South Asian (SAS) AF: 0.0361 AC: 174 AN: 4822

European-Finnish (FIN) AF: 0.00754 AC: 80 AN: 10616

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.0387 AC: 2629 AN: 68020

Other (OTH) AF: 0.0539 AC: 114 AN: 2116

Alfa AF: 0.0453 Hom.: 777

Bravo AF: 0.0596

Asia WGS AF: 0.0640 AC: 221 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.74
DANN	Benign	0.38
PhyloP100		-0.22

Splicing

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

Other links and lift over

dbSNP: rs9900808; hg19: chr17-13062795;