rs1073229

Variant names:

• chr13-30169332-T-C
• rs1073229

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 0.097 in 152,222 control chromosomes in the GnomAD database, including 1,379 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 0.097 (1379 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.184
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.314 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: 0.0969 AC: 14744 AN: 152104 Hom.: 1381 Cov.: 32

Gnomad AFR AF: 0.200

Gnomad AMI AF: 0.0274

Gnomad AMR AF: 0.148

Gnomad ASJ AF: 0.0112

Gnomad EAS AF: 0.327

Gnomad SAS AF: 0.0554

Gnomad FIN AF: 0.0292

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0248

Gnomad OTH AF: 0.0850

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

GnomAD4 genome AF: 0.0970 AC: 14758 AN: 152222 Hom.: 1379 Cov.: 32 AF XY: 0.0993 AC XY: 7390 AN XY: 74442

African (AFR) AF: 0.200 AC: 8292 AN: 41532

American (AMR) AF: 0.148 AC: 2261 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0112 AC: 39 AN: 3468

East Asian (EAS) AF: 0.327 AC: 1695 AN: 5182

South Asian (SAS) AF: 0.0547 AC: 263 AN: 4812

European-Finnish (FIN) AF: 0.0292 AC: 310 AN: 10604

Middle Eastern (MID) AF: 0.0374 AC: 11 AN: 294

European-Non Finnish (NFE) AF: 0.0248 AC: 1684 AN: 68010

Other (OTH) AF: 0.0841 AC: 178 AN: 2116

Alfa AF: 0.0691 Hom.: 351

Bravo AF: 0.112

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.4
DANN	Benign	0.75
PhyloP100		0.18

Splicing

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

Other links and lift over

dbSNP: rs1073229; hg19: chr13-30743469;