chr13-97884609-A-G

Variant names:

• chr13-97884609-A-G
• rs9517112

Variant summary

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

The variant allele was found at a frequency of 0.489 in 152,082 control chromosomes in the GnomAD database, including 22,251 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 0.49 (22251 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.789
• Publications: 1 publications found

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 (AFR) allele frequency at 95% confidence interval = 0.821 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

Frequencies

GnomAD3 genomes AF: 0.488 AC: 74186 AN: 151964 Hom.: 22192 Cov.: 32

Gnomad AFR AF: 0.828

Gnomad AMI AF: 0.522

Gnomad AMR AF: 0.400

Gnomad ASJ AF: 0.404

Gnomad EAS AF: 0.776

Gnomad SAS AF: 0.444

Gnomad FIN AF: 0.295

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.316

Gnomad OTH AF: 0.506

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

GnomAD4 genome AF: 0.489 AC: 74305 AN: 152082 Hom.: 22251 Cov.: 32 AF XY: 0.487 AC XY: 36205 AN XY: 74340

African (AFR) AF: 0.828 AC: 34371 AN: 41496

American (AMR) AF: 0.399 AC: 6104 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.404 AC: 1399 AN: 3466

East Asian (EAS) AF: 0.776 AC: 4016 AN: 5176

South Asian (SAS) AF: 0.445 AC: 2139 AN: 4812

European-Finnish (FIN) AF: 0.295 AC: 3113 AN: 10564

Middle Eastern (MID) AF: 0.503 AC: 148 AN: 294

European-Non Finnish (NFE) AF: 0.316 AC: 21463 AN: 67968

Other (OTH) AF: 0.509 AC: 1078 AN: 2116

Alfa AF: 0.323 Hom.: 4103

Bravo AF: 0.514

Asia WGS AF: 0.624 AC: 2167 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.39
DANN	Benign	0.53
PhyloP100		-0.79

Splicing

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

Other links and lift over

dbSNP: rs9517112; hg19: chr13-98536863; COSMIC: COSV71848094;