5-2191323-T-C

Variant names:

• chr5-2191323-T-C
• rs11133935

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 0.642 in 152,044 control chromosomes in the GnomAD database, including 31,545 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 0.64 (31545 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.880
• Publications: 8 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 (AMR) allele frequency at 95% confidence interval = 0.689 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.642 AC: 97490 AN: 151926 Hom.: 31510 Cov.: 33

Gnomad AFR AF: 0.667

Gnomad AMI AF: 0.443

Gnomad AMR AF: 0.700

Gnomad ASJ AF: 0.647

Gnomad EAS AF: 0.611

Gnomad SAS AF: 0.401

Gnomad FIN AF: 0.658

Gnomad MID AF: 0.614

Gnomad NFE AF: 0.632

Gnomad OTH AF: 0.645

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

GnomAD4 genome AF: 0.642 AC: 97571 AN: 152044 Hom.: 31545 Cov.: 33 AF XY: 0.638 AC XY: 47372 AN XY: 74302

African (AFR) AF: 0.667 AC: 27667 AN: 41452

American (AMR) AF: 0.700 AC: 10710 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.647 AC: 2245 AN: 3472

East Asian (EAS) AF: 0.611 AC: 3148 AN: 5156

South Asian (SAS) AF: 0.400 AC: 1925 AN: 4818

European-Finnish (FIN) AF: 0.658 AC: 6949 AN: 10556

Middle Eastern (MID) AF: 0.616 AC: 181 AN: 294

European-Non Finnish (NFE) AF: 0.632 AC: 42988 AN: 67978

Other (OTH) AF: 0.641 AC: 1355 AN: 2114

Alfa AF: 0.636 Hom.: 108290

Bravo AF: 0.652

Asia WGS AF: 0.516 AC: 1797 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.034
DANN	Benign	0.24
PhyloP100		-0.88

Splicing

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

Other links and lift over

dbSNP: rs11133935; hg19: chr5-2191437;