rs1328244

Variant names:

• chr13-109431551-G-A
• rs1328244

Your query was ambiguous. Multiple possible variants found:

• chr13-109431551-G-A
• chr13-109431551-G-C
• chr13-109431551-G-T

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 0.855 in 152,228 control chromosomes in the GnomAD database, including 56,354 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 0.86 (56354 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.06
• Publications: 3 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 (EAS) allele frequency at 95% confidence interval = 0.977 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: 0.855 AC: 130077 AN: 152112 Hom.: 56302 Cov.: 33

Gnomad AFR AF: 0.701

Gnomad AMI AF: 0.941

Gnomad AMR AF: 0.918

Gnomad ASJ AF: 0.856

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.905

Gnomad FIN AF: 0.917

Gnomad MID AF: 0.886

Gnomad NFE AF: 0.909

Gnomad OTH AF: 0.872

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

GnomAD4 genome AF: 0.855 AC: 130182 AN: 152228 Hom.: 56354 Cov.: 33 AF XY: 0.859 AC XY: 63918 AN XY: 74430

African (AFR) AF: 0.702 AC: 29121 AN: 41504

American (AMR) AF: 0.918 AC: 14045 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.856 AC: 2973 AN: 3472

East Asian (EAS) AF: 1.00 AC: 5188 AN: 5190

South Asian (SAS) AF: 0.904 AC: 4363 AN: 4824

European-Finnish (FIN) AF: 0.917 AC: 9740 AN: 10616

Middle Eastern (MID) AF: 0.884 AC: 260 AN: 294

European-Non Finnish (NFE) AF: 0.909 AC: 61790 AN: 68010

Other (OTH) AF: 0.874 AC: 1844 AN: 2110

Alfa AF: 0.893 Hom.: 101062

Bravo AF: 0.849

Asia WGS AF: 0.961 AC: 3341 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	0.14
DANN	Benign	0.36
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs1328244; hg19: chr13-110083898;