rs1938672

Variant names:

• chr11-58361580-C-T
• rs1938672

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 0.285 in 151,710 control chromosomes in the GnomAD database, including 6,780 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 0.28 (6780 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.463
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.365 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: 0.285 AC: 43195 AN: 151590 Hom.: 6781 Cov.: 31

Gnomad AFR AF: 0.157

Gnomad AMI AF: 0.323

Gnomad AMR AF: 0.248

Gnomad ASJ AF: 0.348

Gnomad EAS AF: 0.147

Gnomad SAS AF: 0.303

Gnomad FIN AF: 0.340

Gnomad MID AF: 0.341

Gnomad NFE AF: 0.368

Gnomad OTH AF: 0.277

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

GnomAD4 genome AF: 0.285 AC: 43201 AN: 151710 Hom.: 6780 Cov.: 31 AF XY: 0.282 AC XY: 20896 AN XY: 74100

African (AFR) AF: 0.156 AC: 6485 AN: 41444

American (AMR) AF: 0.248 AC: 3763 AN: 15190

Ashkenazi Jewish (ASJ) AF: 0.348 AC: 1206 AN: 3468

East Asian (EAS) AF: 0.147 AC: 756 AN: 5152

South Asian (SAS) AF: 0.304 AC: 1460 AN: 4810

European-Finnish (FIN) AF: 0.340 AC: 3576 AN: 10526

Middle Eastern (MID) AF: 0.346 AC: 101 AN: 292

European-Non Finnish (NFE) AF: 0.368 AC: 24983 AN: 67820

Other (OTH) AF: 0.275 AC: 578 AN: 2100

Alfa AF: 0.342 Hom.: 15434

Bravo AF: 0.270

Asia WGS AF: 0.255 AC: 890 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.98
DANN	Benign	0.63
PhyloP100		-0.46

Splicing

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

Other links and lift over

dbSNP: rs1938672; hg19: chr11-58129053;