rs2323266

Variant names:

• chr13-61391170-T-G
• rs2323266

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 0.156 in 152,122 control chromosomes in the GnomAD database, including 2,097 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 0.16 (2097 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.83
• Publications: 6 publications found

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 = 0.205 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: 0.155 AC: 23636 AN: 152002 Hom.: 2088 Cov.: 32

Gnomad AFR AF: 0.0767

Gnomad AMI AF: 0.212

Gnomad AMR AF: 0.112

Gnomad ASJ AF: 0.150

Gnomad EAS AF: 0.136

Gnomad SAS AF: 0.167

Gnomad FIN AF: 0.192

Gnomad MID AF: 0.239

Gnomad NFE AF: 0.208

Gnomad OTH AF: 0.152

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

GnomAD4 genome AF: 0.156 AC: 23675 AN: 152122 Hom.: 2097 Cov.: 32 AF XY: 0.155 AC XY: 11493 AN XY: 74352

African (AFR) AF: 0.0770 AC: 3198 AN: 41530

American (AMR) AF: 0.112 AC: 1710 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.150 AC: 519 AN: 3466

East Asian (EAS) AF: 0.136 AC: 704 AN: 5158

South Asian (SAS) AF: 0.168 AC: 808 AN: 4820

European-Finnish (FIN) AF: 0.192 AC: 2029 AN: 10590

Middle Eastern (MID) AF: 0.243 AC: 71 AN: 292

European-Non Finnish (NFE) AF: 0.208 AC: 14105 AN: 67966

Other (OTH) AF: 0.160 AC: 338 AN: 2110

Alfa AF: 0.184 Hom.: 5694

Bravo AF: 0.144

Asia WGS AF: 0.141 AC: 490 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.095
DANN	Benign	0.38
PhyloP100		-4.8

Splicing

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

Other links and lift over

dbSNP: rs2323266; hg19: chr13-61965303;