rs1124204

Variant names:

• chr13-72580085-G-A
• rs1124204

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 0.442 in 151,970 control chromosomes in the GnomAD database, including 15,562 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 0.44 (15562 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.292
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.59).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.524 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: 0.442 AC: 67101 AN: 151850 Hom.: 15550 Cov.: 32

Gnomad AFR AF: 0.301

Gnomad AMI AF: 0.551

Gnomad AMR AF: 0.533

Gnomad ASJ AF: 0.439

Gnomad EAS AF: 0.407

Gnomad SAS AF: 0.436

Gnomad FIN AF: 0.507

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.499

Gnomad OTH AF: 0.446

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

GnomAD4 genome AF: 0.442 AC: 67150 AN: 151970 Hom.: 15562 Cov.: 32 AF XY: 0.443 AC XY: 32872 AN XY: 74240

African (AFR) AF: 0.301 AC: 12488 AN: 41474

American (AMR) AF: 0.534 AC: 8145 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.439 AC: 1523 AN: 3470

East Asian (EAS) AF: 0.408 AC: 2102 AN: 5154

South Asian (SAS) AF: 0.435 AC: 2092 AN: 4806

European-Finnish (FIN) AF: 0.507 AC: 5341 AN: 10540

Middle Eastern (MID) AF: 0.367 AC: 108 AN: 294

European-Non Finnish (NFE) AF: 0.499 AC: 33908 AN: 67952

Other (OTH) AF: 0.447 AC: 942 AN: 2106

Alfa AF: 0.483 Hom.: 30287

Bravo AF: 0.439

Asia WGS AF: 0.419 AC: 1458 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.59
CADD	Benign	11
DANN	Benign	0.79
PhyloP100		0.29

Splicing

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

Other links and lift over

dbSNP: rs1124204; hg19: chr13-73154223;